Tohidul: does Seasol prime gene expression
Mark Ziemann
2021-03-25
Source codes: https://github.com/markziemann/tohidul_rnaseq
Background
Here we have n=6 control (control “H”) and n=6 seaweed (SW). We have separate leaf and root samples.
Reads underwent quality trimming using Skewer (Jiang et al, 2014). I mapped the reads to the Arabidopsis transcriptome (TAIR10/Ensembl47) using Kallisto (Bray et al, 2016). Expression counts were loaded into R and then DE analysis was performed with DESeq2 (Love et al, 2014). Enrichment analysis was performed using Plant Reactome genesets with the Mitch package (Kaspi & Ziemann 2020).
suppressPackageStartupMessages({
library("reshape2")
library("gplots")
library("DESeq2")
library("mitch")
library("kableExtra")
library("eulerr")
library("UpSetR")
library("vioplot")
})Load data
Here we load the data in from the aligner. Take note that the columns are arranged in order.
tmp <- read.table("3col.tsv.gz")
x <- as.data.frame(acast(tmp, V2~V1, value.var="V3"))
x$gene <- sapply(strsplit(rownames(x),"\\."),"[[",1)
xx <- aggregate(. ~ gene, x, sum)
rownames(xx) <- xx$gene
xx$gene = NULL
xx <- xx[,order(colnames(xx))]
write.table(xx,file="seasol_2021-03_genecounts.tsv",sep="\t",quote=FALSE)Sample sheet
The sample sheet is read in and put in order as well.
ss <- read.table("samplesheet.tsv",header=TRUE,sep="\t")
ss <- ss[order(ss$sample),]MDS
MDS is just like PCA. The more similar (correlated) the data sets are the closer they will appear on the scatterplot.
cols <- as.numeric(factor(ss$tissue))
cols <- gsub(1,"pink",cols)
cols <- gsub(2,"lightblue",cols)
plot(cmdscale(dist(t(xx))), xlab="Coordinate 1", ylab="Coordinate 2",
col=cols, cex=4 , pch=19, main="MDS plot all samples",bty="n")
plot(cmdscale(dist(t(xx))), xlab="Coordinate 1", ylab="Coordinate 2",
col=cols, cex=4 , pch=19, main="MDS plot all samples",bty="n")
text(cmdscale(dist(t(xx))), labels=colnames(xx) )
leaf <- xx[,grep("-L",colnames(xx))]
ssl <- subset(ss,tissue=="leaf")
cols <- as.numeric(factor(ssl$treatment))
cols <- gsub(1,"pink",cols)
cols <- gsub(2,"lightblue",cols)
plot(cmdscale(dist(t(leaf))), xlab="Coordinate 1", ylab="Coordinate 2",
col=cols, cex=4 , main="MDS plot leaf samples",pch=19,bty="n")
text(cmdscale(dist(t(leaf))), labels=colnames(leaf) )
root <- xx[,grep("-R",colnames(xx))]
ssr <- subset(ss,tissue=="root")
cols <- as.numeric(factor(ssr$treatment))
cols <- gsub(1,"pink",cols)
cols <- gsub(2,"lightblue",cols)
plot(cmdscale(dist(t(root))), xlab="Coordinate 1", ylab="Coordinate 2",
col=cols, cex=4 , main="MDS plot root samples",pch=19,bty="n")
text(cmdscale(dist(t(root))), labels=colnames(root) )
colfunc <- colorRampPalette(c("white","blue"))
heatmap.2(cor(xx,method="pearson"),col=colfunc(25),trace="none",
scale="none",margin=c(10,10),main="Pearson correlation all samples")
heatmap.2(cor(xx,method="spearman"),col=colfunc(25),trace="none",
scale="none",margin=c(10,10),main="Spearman correlation all samples")
heatmap.2(cor(leaf,method="pearson"),col=colfunc(25),trace="none",
scale="none",margin=c(10,10),main="Pearson correlation leaf samples")
heatmap.2(cor(leaf,method="spearman"),col=colfunc(25),trace="none",
scale="none",margin=c(10,10),main="Spearman correlation leaf samples")
heatmap.2(cor(root,method="pearson"),col=colfunc(25),trace="none",
scale="none",margin=c(10,10),main="Pearson correlation root samples")
heatmap.2(cor(root,method="spearman"),col=colfunc(25),trace="none",
scale="none",margin=c(10,10),main="Spearman correlation root samples")
Functions
run_de <- function(ss,xx){
xx <- xx[which(rowMeans(xx)>10),]
y <- round(xx)
# MDS
mds <- cmdscale(dist(t(y)))
XMAX=max(mds[,1])*1.1
XMIN=min(mds[,1])*1.1
plot( mds , xlab="Coordinate 1", ylab="Coordinate 2",
type = "n" , xlim=c(XMIN,XMAX),main="MDS plot",bty="n")
text(mds, labels=colnames(y) )
# DE
dds <- DESeqDataSetFromMatrix(countData=y, colData = ss, design = ~ trt)
dds <- DESeq(dds)
de <- DESeq2::results(dds)
de <- de[order(de$pvalue),]
up <- rownames(subset(de, log2FoldChange>0 & padj<0.05 ))
dn <- rownames(subset(de, log2FoldChange<0 & padj<0.05 ))
str(up)
str(dn)
# MA plot
sig <-subset(de, padj < 0.05 )
GENESUP <- length(up)
GENESDN <- length(dn)
SUBHEADER = paste(GENESUP, "up, ", GENESDN, "down")
ns <-subset(de, padj > 0.05 )
plot(log2(de$baseMean),de$log2FoldChange,
xlab="log2 basemean", ylab="log2 foldchange",
pch=19, cex=0.5, col="dark gray",
main="smear plot")
points(log2(sig$baseMean),sig$log2FoldChange,
pch=19, cex=0.5, col="red")
mtext(SUBHEADER)
# heatmap
yn <- y/colSums(y)*1000000
yf <- yn[which(rownames(yn) %in% rownames(de)[1:50]),]
mycols <- gsub("0","yellow",ss$trt)
mycols <- gsub("1","orange",mycols)
colfunc <- colorRampPalette(c("blue", "white", "red"))
heatmap.2( as.matrix(yf), col=colfunc(25),scale="row",
ColSideColors =mycols ,trace="none",
margin = c(10,10), cexRow=0.6, cexCol=0.8 , main="Top 50 genes by p-val")
mtext("yellow=ctrl, orange=trt")
return(de)
}
mitch_barplot <- function(res){
sig <- res$enrichment_result
sig <- head( sig[order(sig$pANOVA),] ,30)
sig <- sig[order(sig$s.dist),]
par(mar=c(3,25,1,1)); barplot(sig$s.dist,horiz=TRUE,las=2,cex.names = 0.6,cex.axis = 0.6,
names.arg=sig$set,main="Enrichment score") ;grid()
}Split data into contrast groups
l3 <- leaf[,grep("3D",colnames(leaf))]
ssl3 <- subset(ssl,days==3)
ssl3$trt <- as.numeric(ssl3$treatment == "seaweed")
l5 <- leaf[,grep("5D",colnames(leaf))]
ssl5 <- subset(ssl,days==5)
ssl5$trt <- as.numeric(ssl5$treatment == "seaweed")
r3 <- root[,grep("3D",colnames(root))]
ssr3 <- subset(ssr,days==3)
ssr3$trt <- as.numeric(ssr3$treatment == "seaweed")
r5 <- root[,grep("5D",colnames(root))]
ssr5 <- subset(ssr,days==5)
ssr5$trt <- as.numeric(ssr5$treatment == "seaweed")DE
Here, were using DESeq2 to perform differential expression analysis to understand gene expression changes caused by seaweed treatment. Enrichment analysis is performed with mitch.
del3 <- run_de(ssl3,l3)## converting counts to integer mode## the design formula contains one or more numeric variables with integer values,
## specifying a model with increasing fold change for higher values.
## did you mean for this to be a factor? if so, first convert
## this variable to a factor using the factor() function## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## chr [1:523] "AT1G80315" "AT2G47880" "AT3G03475" "AT4G39250" "AT2G02780" ...
## chr [1:727] "AT4G02720" "AT1G80890" "AT4G23680" "AT1G19840" "AT3G08520" ...
del5 <- run_de(ssl5,l5)## converting counts to integer mode## the design formula contains one or more numeric variables with integer values,
## specifying a model with increasing fold change for higher values.
## did you mean for this to be a factor? if so, first convert
## this variable to a factor using the factor() function## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## chr [1:1988] "AT2G47880" "AT5G48485" "AT1G25530" "AT4G12290" "AT5G43780" ...
## chr [1:1871] "AT5G38910" "AT5G38200" "AT2G26695" "AT5G12930" "AT1G78000" ...
der3 <- run_de(ssr3,r3)## converting counts to integer mode## the design formula contains one or more numeric variables with integer values,
## specifying a model with increasing fold change for higher values.
## did you mean for this to be a factor? if so, first convert
## this variable to a factor using the factor() function## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## chr [1:1184] "AT1G01580" "AT5G43780" "AT2G28160" "AT4G11310" "AT1G08090" ...
## chr [1:1250] "AT5G38910" "AT4G19810" "AT5G39100" "AT2G46750" "AT2G26695" ...
der5 <- run_de(ssr5,r5)## converting counts to integer mode## the design formula contains one or more numeric variables with integer values,
## specifying a model with increasing fold change for higher values.
## did you mean for this to be a factor? if so, first convert
## this variable to a factor using the factor() function## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing
## chr [1:1756] "AT4G11310" "AT5G43780" "AT4G40070" "AT1G08090" "AT2G42600" ...
## chr [1:2236] "AT4G31330" "AT5G38910" "AT5G48850" "AT4G19810" "AT1G04770" ...
del3_top <- head(as.data.frame(del3),40)
kbl(del3_top[order(del3_top$log2FoldChange),]) %>% kable_paper("hover", full_width = F)| baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | |
|---|---|---|---|---|---|---|
| AT4G02720 | 66.16392 | -24.4034082 | 3.0036045 | -8.124708 | 0e+00 | 0.0000000 |
| AT1G19840 | 291.69712 | -1.4409964 | 0.2429784 | -5.930554 | 0e+00 | 0.0000065 |
| AT5G47450 | 276.10344 | -1.2830545 | 0.2441999 | -5.254115 | 1e-07 | 0.0001110 |
| AT1G23100 | 85.04869 | -1.2208587 | 0.2146863 | -5.686709 | 0e+00 | 0.0000187 |
| AT1G17180 | 68.68431 | -1.1545629 | 0.2265703 | -5.095825 | 3e-07 | 0.0002147 |
| AT2G32190 | 267.07153 | -1.1038402 | 0.2203213 | -5.010139 | 5e-07 | 0.0003014 |
| AT3G20470 | 1079.97814 | -1.0498895 | 0.1994738 | -5.263296 | 1e-07 | 0.0001094 |
| AT4G23680 | 1266.99560 | -1.0248529 | 0.1681192 | -6.095990 | 0e+00 | 0.0000029 |
| AT5G13210 | 278.36365 | -0.9339612 | 0.1865855 | -5.005540 | 6e-07 | 0.0003014 |
| AT4G36900 | 1746.59742 | -0.7128679 | 0.1350567 | -5.278286 | 1e-07 | 0.0001094 |
| AT5G57290 | 3366.65592 | -0.5135223 | 0.0928413 | -5.531182 | 0e+00 | 0.0000382 |
| AT3G08520 | 1267.73717 | -0.4746525 | 0.0813519 | -5.834556 | 0e+00 | 0.0000090 |
| AT3G62130 | 1533.90912 | -0.4674869 | 0.0864150 | -5.409791 | 1e-07 | 0.0000621 |
| AT1G67870 | 19995.45754 | -0.4608692 | 0.0902687 | -5.105527 | 3e-07 | 0.0002147 |
| AT1G80890 | 628.10119 | -0.4586752 | 0.0736640 | -6.226587 | 0e+00 | 0.0000015 |
| AT2G47690 | 1511.32865 | -0.4519945 | 0.0807325 | -5.598670 | 0e+00 | 0.0000275 |
| AT1G76010 | 5052.13968 | -0.4199074 | 0.0761585 | -5.513600 | 0e+00 | 0.0000400 |
| AT4G34265 | 1691.95506 | -0.4114401 | 0.0775696 | -5.304139 | 1e-07 | 0.0001023 |
| AT1G74230 | 3898.09059 | -0.3939446 | 0.0747873 | -5.267536 | 1e-07 | 0.0001094 |
| AT1G19600 | 1838.07028 | -0.3571698 | 0.0684762 | -5.215970 | 2e-07 | 0.0001319 |
| AT3G06210 | 1470.34765 | -0.2634517 | 0.0519776 | -5.068557 | 4e-07 | 0.0002410 |
| AT1G71070 | 1062.69043 | 0.2706672 | 0.0538989 | 5.021759 | 5e-07 | 0.0002916 |
| AT2G02780 | 636.45222 | 0.4509858 | 0.0723853 | 6.230351 | 0e+00 | 0.0000015 |
| AT2G22860 | 161.81028 | 0.8072323 | 0.1599779 | 5.045899 | 5e-07 | 0.0002640 |
| AT2G07515 | 214.78725 | 0.8315503 | 0.1411136 | 5.892772 | 0e+00 | 0.0000075 |
| AT1G52800 | 469.12466 | 0.8952334 | 0.1754993 | 5.101066 | 3e-07 | 0.0002147 |
| AT5G01600 | 32677.05475 | 0.9136887 | 0.1663680 | 5.491974 | 0e+00 | 0.0000430 |
| AT3G03910 | 109.71299 | 1.1725394 | 0.2299936 | 5.098140 | 3e-07 | 0.0002147 |
| AT4G31398 | 64.01317 | 1.2809470 | 0.2194899 | 5.836017 | 0e+00 | 0.0000090 |
| AT2G47880 | 786.08493 | 1.5068399 | 0.2382290 | 6.325173 | 0e+00 | 0.0000015 |
| AT3G46130 | 370.59654 | 1.5509200 | 0.2924201 | 5.303740 | 1e-07 | 0.0001023 |
| AT3G15270 | 90.76513 | 1.9224787 | 0.3651632 | 5.264711 | 1e-07 | 0.0001094 |
| AT4G31355 | 47.78863 | 1.9311220 | 0.3563366 | 5.419377 | 1e-07 | 0.0000616 |
| AT3G04200 | 21.61338 | 2.2999200 | 0.4503893 | 5.106516 | 3e-07 | 0.0002147 |
| AT4G34950 | 1829.83099 | 2.4086321 | 0.4291084 | 5.613109 | 0e+00 | 0.0000269 |
| AT1G19250 | 217.07772 | 2.8340195 | 0.4893375 | 5.791543 | 0e+00 | 0.0000108 |
| AT4G28755 | 960.99527 | 2.9704518 | 0.4964202 | 5.983745 | 0e+00 | 0.0000052 |
| AT4G39250 | 36.27526 | 3.3240394 | 0.5329771 | 6.236740 | 0e+00 | 0.0000015 |
| AT3G03475 | 50.00135 | 5.2471854 | 0.8406155 | 6.242075 | 0e+00 | 0.0000015 |
| AT1G80315 | 91.57447 | 23.0677521 | 3.0034965 | 7.680299 | 0e+00 | 0.0000000 |
del5_top <- head(as.data.frame(del5),40)
kbl(del5_top[order(del5_top$log2FoldChange),]) %>% kable_paper("hover", full_width = F)| baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | |
|---|---|---|---|---|---|---|
| AT5G38910 | 303.26845 | -4.5009302 | 0.2310328 | -19.48178 | 0 | 0 |
| AT1G12030 | 89.36669 | -3.5522698 | 0.3386993 | -10.48797 | 0 | 0 |
| AT1G73120 | 1036.14069 | -3.3322915 | 0.2491372 | -13.37532 | 0 | 0 |
| AT5G48850 | 3419.08872 | -3.2697161 | 0.3002950 | -10.88835 | 0 | 0 |
| AT3G05400 | 846.00860 | -3.0653540 | 0.2463154 | -12.44483 | 0 | 0 |
| AT2G26695 | 693.06424 | -2.8309548 | 0.1785465 | -15.85556 | 0 | 0 |
| AT3G49580 | 4087.75337 | -2.7393679 | 0.2163430 | -12.66215 | 0 | 0 |
| AT1G78000 | 1862.46954 | -2.6848892 | 0.1789891 | -15.00029 | 0 | 0 |
| AT4G35720 | 254.69296 | -2.6030184 | 0.2421016 | -10.75176 | 0 | 0 |
| AT3G08860 | 7386.45120 | -2.5836240 | 0.1813327 | -14.24798 | 0 | 0 |
| AT5G38200 | 1192.11772 | -2.2014601 | 0.1268514 | -17.35464 | 0 | 0 |
| AT4G34710 | 56680.08013 | -2.1992463 | 0.2080118 | -10.57270 | 0 | 0 |
| AT3G49570 | 1328.65439 | -2.1710039 | 0.1962809 | -11.06070 | 0 | 0 |
| AT1G23730 | 1053.73159 | -2.1490758 | 0.1878390 | -11.44105 | 0 | 0 |
| AT3G50400 | 874.95029 | -1.9552630 | 0.1534391 | -12.74293 | 0 | 0 |
| AT4G04830 | 3051.95054 | -1.9477840 | 0.1378509 | -14.12964 | 0 | 0 |
| AT2G31980 | 301.82419 | -1.9016190 | 0.1662060 | -11.44134 | 0 | 0 |
| AT1G22500 | 1328.15939 | -1.8245820 | 0.1289409 | -14.15053 | 0 | 0 |
| AT5G13900 | 335.30680 | -1.7263737 | 0.1221029 | -14.13868 | 0 | 0 |
| AT5G13580 | 1077.09671 | -1.5801901 | 0.1508742 | -10.47356 | 0 | 0 |
| AT4G39675 | 214.68248 | -1.5360999 | 0.1107444 | -13.87068 | 0 | 0 |
| AT1G70170 | 201.84955 | -1.4899895 | 0.1419187 | -10.49890 | 0 | 0 |
| AT5G50260 | 414.42698 | -1.3728441 | 0.1001932 | -13.70197 | 0 | 0 |
| AT5G12930 | 337.50418 | -1.3686025 | 0.0906511 | -15.09747 | 0 | 0 |
| AT1G56320 | 212.24014 | -1.3601830 | 0.1266107 | -10.74304 | 0 | 0 |
| AT5G51200 | 5510.61669 | -1.2330745 | 0.1176633 | -10.47969 | 0 | 0 |
| AT5G19600 | 1087.89214 | -1.1927369 | 0.1149157 | -10.37923 | 0 | 0 |
| AT2G40390 | 322.95200 | -1.1331409 | 0.1092327 | -10.37364 | 0 | 0 |
| AT5G11090 | 4248.59915 | -1.0310354 | 0.0719042 | -14.33901 | 0 | 0 |
| AT4G33740 | 2818.09900 | -0.6062258 | 0.0547852 | -11.06551 | 0 | 0 |
| AT4G12290 | 11742.50005 | 0.6076344 | 0.0517994 | 11.73053 | 0 | 0 |
| AT3G20390 | 6799.64674 | 1.0014177 | 0.0967891 | 10.34639 | 0 | 0 |
| AT5G43780 | 4091.03656 | 1.1249149 | 0.0970683 | 11.58890 | 0 | 0 |
| AT1G70260 | 1138.66771 | 1.5134765 | 0.1350173 | 11.20950 | 0 | 0 |
| AT2G47880 | 845.61213 | 1.6231847 | 0.1005597 | 16.14150 | 0 | 0 |
| AT1G25530 | 599.99203 | 1.6376964 | 0.1388451 | 11.79513 | 0 | 0 |
| AT3G54600 | 3893.10989 | 1.9644164 | 0.1883688 | 10.42857 | 0 | 0 |
| AT4G13770 | 17921.05976 | 2.2957121 | 0.2032233 | 11.29650 | 0 | 0 |
| AT5G07690 | 468.10996 | 2.8212623 | 0.2751824 | 10.25233 | 0 | 0 |
| AT5G48485 | 151.59769 | 10.6972566 | 0.8895426 | 12.02557 | 0 | 0 |
der3_top <- head(as.data.frame(der3),40)
kbl(der3_top[order(der3_top$log2FoldChange),]) %>% kable_paper("hover", full_width = F)| baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | |
|---|---|---|---|---|---|---|
| AT5G38910 | 7598.75697 | -4.132285 | 0.1816282 | -22.75135 | 0 | 0 |
| AT3G49580 | 600.84811 | -3.834888 | 0.2627172 | -14.59702 | 0 | 0 |
| AT5G39110 | 282.44729 | -3.336999 | 0.2338947 | -14.26710 | 0 | 0 |
| AT2G26695 | 386.58348 | -3.072421 | 0.2062841 | -14.89412 | 0 | 0 |
| AT2G27120 | 209.43829 | -3.019986 | 0.2285976 | -13.21093 | 0 | 0 |
| AT2G13810 | 522.56436 | -2.877543 | 0.2037820 | -14.12069 | 0 | 0 |
| AT3G49570 | 516.68640 | -2.797519 | 0.1905353 | -14.68242 | 0 | 0 |
| AT5G48850 | 1997.98469 | -2.597651 | 0.1930681 | -13.45458 | 0 | 0 |
| AT2G02120 | 284.10026 | -2.283909 | 0.2010628 | -11.35918 | 0 | 0 |
| AT5G39100 | 1315.19054 | -2.199009 | 0.1419332 | -15.49327 | 0 | 0 |
| AT5G39120 | 418.19064 | -2.182258 | 0.1543712 | -14.13644 | 0 | 0 |
| AT4G10500 | 1169.67223 | -2.155053 | 0.1836628 | -11.73374 | 0 | 0 |
| AT2G46750 | 3232.91881 | -1.977160 | 0.1278050 | -15.47013 | 0 | 0 |
| AT2G20180 | 639.44472 | -1.947967 | 0.1463537 | -13.30999 | 0 | 0 |
| AT4G31330 | 563.89103 | -1.933138 | 0.1464658 | -13.19856 | 0 | 0 |
| AT2G18480 | 3130.78791 | -1.893936 | 0.1634834 | -11.58488 | 0 | 0 |
| AT4G19810 | 3581.47308 | -1.833642 | 0.1047939 | -17.49761 | 0 | 0 |
| AT2G43590 | 2203.62549 | -1.787368 | 0.1291559 | -13.83884 | 0 | 0 |
| AT1G19960 | 1118.82562 | -1.652099 | 0.1489457 | -11.09196 | 0 | 0 |
| AT1G05340 | 1342.74096 | -1.580612 | 0.1348598 | -11.72041 | 0 | 0 |
| AT4G34710 | 39842.61929 | -1.496570 | 0.1034954 | -14.46026 | 0 | 0 |
| AT1G04770 | 1508.85727 | -1.454794 | 0.1318441 | -11.03419 | 0 | 0 |
| AT4G02360 | 354.27690 | -1.437689 | 0.1104669 | -13.01466 | 0 | 0 |
| AT2G26560 | 1508.34170 | -1.311356 | 0.1108042 | -11.83490 | 0 | 0 |
| AT1G18100 | 2784.50579 | -1.238096 | 0.1081064 | -11.45256 | 0 | 0 |
| AT5G64810 | 803.82367 | -1.220550 | 0.0987636 | -12.35830 | 0 | 0 |
| AT2G26700 | 768.68589 | -1.056769 | 0.0926573 | -11.40513 | 0 | 0 |
| AT5G19600 | 2587.70841 | -1.044058 | 0.0736467 | -14.17657 | 0 | 0 |
| AT5G06860 | 9314.52339 | -1.013486 | 0.0909549 | -11.14273 | 0 | 0 |
| AT4G23680 | 12986.47726 | -1.012964 | 0.0908721 | -11.14714 | 0 | 0 |
| AT2G19060 | 727.07863 | 1.173293 | 0.0965973 | 12.14623 | 0 | 0 |
| AT2G28160 | 1328.74548 | 1.179207 | 0.0850581 | 13.86353 | 0 | 0 |
| AT4G15920 | 1096.98692 | 1.281040 | 0.1088874 | 11.76481 | 0 | 0 |
| AT5G43780 | 30273.02984 | 1.364120 | 0.0952347 | 14.32376 | 0 | 0 |
| AT4G19690 | 4513.66194 | 2.447739 | 0.2008284 | 12.18821 | 0 | 0 |
| AT4G11310 | 262.53106 | 2.594167 | 0.1904828 | 13.61890 | 0 | 0 |
| AT1G08090 | 3090.44759 | 2.659642 | 0.2180453 | 12.19766 | 0 | 0 |
| AT4G31940 | 1443.68798 | 2.731755 | 0.2309461 | 11.82854 | 0 | 0 |
| AT1G01580 | 4176.35859 | 3.005108 | 0.1845510 | 16.28334 | 0 | 0 |
| AT3G12900 | 70.86153 | 4.577524 | 0.4143860 | 11.04652 | 0 | 0 |
der5_top <- head(as.data.frame(der5),40)
kbl(der5_top[order(der5_top$log2FoldChange),]) %>% kable_paper("hover", full_width = F)| baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | |
|---|---|---|---|---|---|---|
| AT3G49580 | 998.83251 | -4.6220779 | 0.3422141 | -13.50639 | 0 | 0 |
| AT5G38910 | 10987.00482 | -3.7457267 | 0.1686275 | -22.21303 | 0 | 0 |
| AT5G48850 | 1807.31329 | -3.1511096 | 0.1431920 | -22.00618 | 0 | 0 |
| AT3G49570 | 587.75367 | -2.9991097 | 0.2019578 | -14.85018 | 0 | 0 |
| AT5G39110 | 839.64900 | -2.9955104 | 0.2180689 | -13.73653 | 0 | 0 |
| AT5G39120 | 909.73284 | -2.8086129 | 0.1568381 | -17.90772 | 0 | 0 |
| AT3G05400 | 108.92280 | -2.6442006 | 0.2117059 | -12.48997 | 0 | 0 |
| AT5G39100 | 2795.92797 | -2.6103582 | 0.1374017 | -18.99800 | 0 | 0 |
| AT4G31330 | 1110.46241 | -2.5304887 | 0.1096315 | -23.08177 | 0 | 0 |
| AT5G39150 | 838.71855 | -2.3448452 | 0.1559560 | -15.03530 | 0 | 0 |
| AT4G19760 | 390.58809 | -2.3141453 | 0.1736434 | -13.32700 | 0 | 0 |
| AT2G30670 | 96.03539 | -2.2548762 | 0.1495304 | -15.07972 | 0 | 0 |
| AT2G18480 | 4361.01455 | -2.2456979 | 0.1502087 | -14.95052 | 0 | 0 |
| AT5G26220 | 692.63311 | -2.1995380 | 0.1683683 | -13.06385 | 0 | 0 |
| AT4G19810 | 4035.62941 | -2.1581835 | 0.1038065 | -20.79044 | 0 | 0 |
| AT4G10500 | 1373.21980 | -2.0488679 | 0.1316222 | -15.56628 | 0 | 0 |
| AT2G46750 | 3670.07518 | -1.9607279 | 0.1209225 | -16.21475 | 0 | 0 |
| AT2G43570 | 920.00023 | -1.8372522 | 0.1292272 | -14.21722 | 0 | 0 |
| AT2G43590 | 1330.43005 | -1.7946152 | 0.1151771 | -15.58136 | 0 | 0 |
| AT1G01190 | 2900.50851 | -1.6264942 | 0.1117185 | -14.55886 | 0 | 0 |
| AT3G16530 | 1868.52543 | -1.5762132 | 0.1152628 | -13.67495 | 0 | 0 |
| AT2G20180 | 473.67899 | -1.5406756 | 0.1049507 | -14.67999 | 0 | 0 |
| AT1G02920 | 6140.46609 | -1.5055580 | 0.1007425 | -14.94462 | 0 | 0 |
| AT1G04770 | 1359.23994 | -1.3825075 | 0.0700510 | -19.73572 | 0 | 0 |
| AT2G15220 | 1912.22184 | -1.3723700 | 0.0926546 | -14.81167 | 0 | 0 |
| AT4G37370 | 368.97029 | -1.3568495 | 0.0984375 | -13.78386 | 0 | 0 |
| AT4G11650 | 9290.05791 | -1.3405558 | 0.0926876 | -14.46317 | 0 | 0 |
| AT3G49120 | 11430.52900 | -1.3335784 | 0.0725349 | -18.38535 | 0 | 0 |
| AT5G06860 | 10880.66530 | -1.1680348 | 0.0798388 | -14.62991 | 0 | 0 |
| AT1G45201 | 7952.66067 | -1.1525154 | 0.0679340 | -16.96522 | 0 | 0 |
| AT1G18100 | 2478.33310 | -1.1411462 | 0.0683744 | -16.68968 | 0 | 0 |
| AT3G04070 | 1138.43994 | -1.1235648 | 0.0759427 | -14.79489 | 0 | 0 |
| AT1G75280 | 6889.75246 | -1.0048075 | 0.0673791 | -14.91276 | 0 | 0 |
| AT4G21990 | 8700.31713 | -0.8852012 | 0.0639897 | -13.83349 | 0 | 0 |
| AT5G57350 | 3674.79494 | -0.8485921 | 0.0553065 | -15.34343 | 0 | 0 |
| AT5G38200 | 3178.00149 | -0.7431379 | 0.0556775 | -13.34720 | 0 | 0 |
| AT4G30960 | 26781.42965 | -0.6194370 | 0.0484161 | -12.79403 | 0 | 0 |
| AT4G40070 | 979.72415 | 1.4005373 | 0.1054872 | 13.27684 | 0 | 0 |
| AT5G43780 | 27353.51856 | 1.6806535 | 0.1192586 | 14.09252 | 0 | 0 |
| AT4G11310 | 286.84164 | 2.5769180 | 0.1671467 | 15.41710 | 0 | 0 |
write.table(del3,file="del3.tsv",quote=FALSE,sep="\t")
write.table(del5,file="del5.tsv",quote=FALSE,sep="\t")
write.table(der3,file="der3.tsv",quote=FALSE,sep="\t")
write.table(der5,file="der5.tsv",quote=FALSE,sep="\t")
del3_up <- rownames(subset(del3,padj<0.05&log2FoldChange>0))
del3_dn <- rownames(subset(del3,padj<0.05&log2FoldChange<0))
del5_up <- rownames(subset(del5,padj<0.05&log2FoldChange>0))
del5_dn <- rownames(subset(del5,padj<0.05&log2FoldChange<0))
der3_up <- rownames(subset(der3,padj<0.05&log2FoldChange>0))
der3_dn <- rownames(subset(der3,padj<0.05&log2FoldChange<0))
der5_up <- rownames(subset(der5,padj<0.05&log2FoldChange>0))
der5_dn <- rownames(subset(der5,padj<0.05&log2FoldChange<0))
up <- sapply(list(del3_up,del5_up,der3_up,der5_up),length)
dn <- sapply(list(del3_dn,del5_dn,der3_dn,der5_dn),length)
res_summary <- data.frame(up,dn,row.names=c("L3","L5","R3","R5"))
res_summary$de <- c("Leaf 3d","Leaf 5d","Root 3d","Root 5d")
kbl(res_summary) %>% kable_paper("hover", full_width = F)| up | dn | de | |
|---|---|---|---|
| L3 | 523 | 727 | Leaf 3d |
| L5 | 1988 | 1871 | Leaf 5d |
| R3 | 1184 | 1250 | Root 3d |
| R5 | 1756 | 2236 | Root 5d |
barplot(res_summary$up,ylim=c(-2500,2500), axes=TRUE, main="number of DEGs up/down")
barplot(-res_summary$dn, add = TRUE, names.arg = rownames(res_summary), axes = FALSE)
Venn diagram plots of overlap
# upregulated genes
v1 <- list("leaf 3d up"=del3_up, "leaf 5d up"=del5_up,
"root 3d up" =der3_up , "root 5d up"=der5_up)
plot(euler(v1),quantities = TRUE)
intersect(del3_up,del5_up)## [1] "AT2G47880" "AT4G39250" "AT4G34950" "AT5G01600" "AT4G31355" "AT3G46130"
## [7] "AT3G15270" "AT3G04200" "AT1G52800" "AT3G03910" "AT2G16660" "AT3G04480"
## [13] "AT1G12320" "AT4G31354" "AT1G73890" "AT5G07690" "AT2G24120" "AT2G28210"
## [19] "AT5G24270" "AT1G29720" "AT2G25220" "AT5G45650" "AT1G05630" "AT2G01023"
## [25] "AT4G22730" "AT1G53160" "AT1G29270" "AT2G40300" "AT4G37080" "AT3G26700"
## [31] "AT4G00140" "AT2G01910" "AT4G00330" "AT3G20110" "AT5G23020" "AT5G23010"
## [37] "AT2G30460" "AT5G07700" "AT3G49160" "AT1G08810" "AT1G72930" "AT1G68585"
## [43] "AT3G05290" "AT1G67865" "AT5G45550" "AT4G00950" "AT2G42880" "AT1G08180"
## [49] "AT4G23130" "AT2G21650" "AT2G44210" "AT3G29810" "AT5G63950" "AT2G23610"
## [55] "AT3G47500" "AT1G16640" "AT3G54600" "AT3G55520" "AT2G19900" "AT1G49620"
## [61] "AT3G56480" "AT1G12330" "AT3G25500" "AT5G55490" "AT4G00670" "AT4G19410"
## [67] "AT3G19720" "AT1G13650" "AT3G23570" "AT5G41140" "AT1G29660" "AT2G18328"
## [73] "AT3G19710" "AT1G25530" "AT1G30490" "AT1G31690" "AT4G32790" "AT1G08090"
## [79] "AT3G26820" "AT4G12140" "AT2G43100" "AT1G72500" "AT3G05900" "AT1G02220"
## [85] "AT3G61310" "AT5G57123" "AT3G11570" "AT1G72610" "AT5G65730" "AT3G06450"
## [91] "AT1G12450" "AT1G09510" "AT2G19780" "AT4G36570" "AT3G26670" "AT1G22690"
## [97] "AT2G42380" "AT4G13770" "AT4G12030" "AT2G26510" "AT1G10120" "AT5G17270"
## [103] "AT3G05910" "AT1G52240" "AT1G54040" "AT3G04810" "AT4G14070" "AT2G24300"
## [109] "AT1G04160" "AT5G43910" "AT4G31408" "AT2G15050" "AT1G60730" "AT4G03050"
## [115] "AT3G09920" "AT4G25350" "AT5G01500" "AT3G60320" "AT4G12290" "AT4G38770"
## [121] "AT4G38950" "AT2G21080" "AT3G14020" "AT1G16410" "AT5G26000" "AT3G23690"
## [127] "AT5G33370" "AT4G08760" "AT4G23060" "AT4G14040" "AT3G62960" "AT1G73060"
## [133] "AT5G49680" "AT5G21105" "AT1G33030" "AT3G08040" "AT3G28930" "AT5G53930"
## [139] "AT2G30010" "AT5G49215" "AT3G03190" "AT1G70940" "AT2G04190" "AT4G39950"
## [145] "AT3G62630" "AT4G11820" "AT4G18760" "AT5G60920" "AT5G16570" "AT5G04160"
## [151] "AT3G04210" "AT3G47450" "AT4G21590" "AT3G59010" "AT4G19020" "AT1G69700"
## [157] "AT1G27840" "AT5G14200" "AT3G24140" "AT2G05760" "AT3G21950" "AT1G70210"
## [163] "AT3G24480" "AT1G75250" "AT5G09300" "AT3G07990" "AT4G01440" "AT3G02020"
## [169] "AT2G43020" "AT5G46420" "AT4G27730" "AT1G58025" "AT2G22330" "AT3G47930"
## [175] "AT1G10020" "AT3G23820" "AT2G01830" "AT4G32410" "AT5G04130" "AT4G25230"
## [181] "AT3G20390" "AT3G01930" "AT2G18890" "AT1G17600" "AT1G16400" "AT4G35900"
## [187] "AT1G70260" "AT4G14750" "AT4G29400" "AT4G18030" "AT1G17920" "AT4G40065"
## [193] "AT1G21440" "AT1G79720" "AT1G60060" "AT4G03820" "AT4G32710" "AT2G25450"
## [199] "AT5G18690" "AT2G36380" "AT1G13270" "AT4G05120" "AT4G05090" "AT5G17390"
## [205] "AT3G58990" "AT2G23600" "AT1G66940" "AT4G40070" "AT5G61950" "at4g13494"
## [211] "AT1G23170" "AT4G16980" "AT3G53100" "AT2G44740" "AT5G55720" "AT1G23180"
## [217] "AT5G64560" "AT4G01430" "AT2G18910" "AT1G65860"intersect(der3_up,der3_up)## [1] "AT1G01580" "AT5G43780" "AT2G28160" "AT4G11310" "AT1G08090" "AT4G19690"
## [7] "AT2G19060" "AT4G31940" "AT4G15920" "AT3G12900" "AT5G24270" "AT5G02180"
## [13] "AT5G40780" "AT3G46280" "AT2G25260" "AT3G18450" "AT5G26300" "AT1G35240"
## [19] "AT3G52190" "AT4G25350" "AT5G38100" "AT3G27950" "AT3G08040" "AT3G10720"
## [25] "AT1G50590" "AT3G61830" "AT1G78120" "AT5G64000" "AT3G07195" "AT3G24290"
## [31] "AT5G62865" "AT1G34047" "AT5G14650" "AT3G02610" "AT5G67450" "AT5G40590"
## [37] "AT5G16570" "AT3G01190" "AT1G73270" "AT2G35270" "AT5G46050" "AT3G55700"
## [43] "AT3G58060" "AT3G23000" "AT3G14280" "AT4G20260" "AT5G48485" "AT2G36690"
## [49] "AT4G15393" "AT1G55940" "AT2G39200" "AT2G38390" "AT3G58810" "AT1G54010"
## [55] "AT4G12090" "AT3G24300" "AT1G49320" "AT1G07690" "AT3G55150" "AT2G32270"
## [61] "AT5G20470" "AT5G25810" "AT3G14225" "AT4G13505" "AT4G30120" "AT3G12820"
## [67] "AT1G11540" "AT3G46130" "AT1G21210" "AT1G69900" "AT2G24010" "AT5G48430"
## [73] "AT4G26050" "AT4G00670" "AT5G67520" "AT4G19925" "AT5G67080" "AT3G63360"
## [79] "AT4G40070" "AT1G49030" "AT1G21230" "AT1G19450" "AT3G50350" "AT3G24503"
## [85] "AT1G01360" "AT4G18940" "AT3G51350" "AT1G47840" "AT5G11610" "AT5G14130"
## [91] "AT5G43590" "AT5G50200" "AT3G61400" "AT4G33720" "AT4G20450" "AT5G45470"
## [97] "AT5G19040" "AT4G33820" "AT3G20110" "AT3G23510" "AT1G15670" "AT1G14210"
## [103] "AT3G60090" "AT1G35242" "AT3G16390" "AT5G33355" "AT4G04955" "AT4G22460"
## [109] "AT1G34040" "AT5G54680" "AT1G73120" "AT5G43910" "AT4G17680" "AT1G30840"
## [115] "AT1G78860" "AT2G28460" "AT1G05250" "AT1G08100" "AT2G19800" "AT5G46040"
## [121] "AT1G29240" "AT1G66930" "AT1G24485" "AT3G26590" "AT1G14550" "AT1G76990"
## [127] "AT5G45280" "AT5G54590" "AT3G59580" "AT4G35040" "AT2G11810" "AT5G56840"
## [133] "AT5G19200" "AT3G61880" "AT2G30010" "AT3G61380" "AT4G08300" "AT2G28210"
## [139] "AT5G45380" "AT3G56970" "AT3G25730" "AT5G05440" "AT4G17870" "AT3G47980"
## [145] "AT5G51310" "AT4G37520" "AT5G03570" "AT5G40210" "AT1G54950" "AT1G17300"
## [151] "AT4G26220" "AT5G24230" "AT1G30370" "AT5G65320" "AT3G51340" "AT3G19680"
## [157] "AT3G23800" "AT3G09922" "AT5G60350" "AT2G02020" "AT1G49310" "AT3G54030"
## [163] "AT5G62730" "AT3G49860" "AT2G29995" "AT1G38131" "AT5G49850" "AT4G26060"
## [169] "AT4G25110" "AT2G28140" "AT2G38310" "AT2G40330" "AT1G24170" "AT5G56080"
## [175] "AT1G27210" "AT1G49100" "AT1G22220" "AT3G07000" "AT5G62420" "AT1G54890"
## [181] "AT2G43140" "AT5G01220" "AT1G14540" "AT3G56980" "AT1G01420" "AT4G36920"
## [187] "AT5G46600" "AT4G30280" "AT2G34080" "AT5G01610" "AT4G14780" "AT4G35060"
## [193] "AT3G29430" "AT5G20400" "AT1G12330" "AT3G49845" "AT2G36255" "AT1G29180"
## [199] "AT1G57680" "AT3G46810" "AT2G42600" "AT2G21880" "AT3G07720" "AT5G38940"
## [205] "AT1G78020" "AT5G54790" "AT4G01750" "AT3G23090" "AT4G36990" "AT2G39530"
## [211] "AT1G06640" "AT5G41180" "AT4G33790" "AT3G46710" "AT3G46800" "AT3G56060"
## [217] "AT2G19190" "AT1G21200" "AT5G28630" "AT3G47110" "AT3G05950" "AT2G23960"
## [223] "AT1G51790" "AT1G23110" "AT5G38820" "AT4G18340" "AT2G30990" "AT5G67210"
## [229] "AT1G35580" "AT5G24100" "AT5G16900" "AT1G80450" "AT1G44170" "AT5G60060"
## [235] "AT3G10870" "AT3G50160" "AT2G17710" "AT1G28570" "AT5G45730" "AT4G05120"
## [241] "AT1G03457" "AT4G01480" "AT3G02580" "AT1G05805" "AT1G05300" "AT2G20142"
## [247] "AT5G06200" "AT3G23730" "AT3G25110" "AT1G53940" "AT1G19390" "AT5G63450"
## [253] "at4g05415" "AT1G29025" "AT5G66690" "AT2G28080" "AT2G29750" "AT3G07940"
## [259] "AT1G48500" "AT1G17090" "AT1G22160" "AT2G47550" "AT1G51800" "AT4G31860"
## [265] "AT5G10520" "AT3G59970" "AT4G00880" "AT4G25420" "AT5G46260" "AT1G76090"
## [271] "AT2G35155" "AT4G06534" "AT3G13610" "AT4G13130" "AT3G13435" "AT5G46330"
## [277] "AT2G19990" "AT3G10980" "AT4G15160" "AT1G21140" "AT2G25680" "AT2G27660"
## [283] "AT5G10290" "AT2G02610" "AT3G13790" "AT5G52830" "AT4G17880" "AT5G03355"
## [289] "AT3G14680" "AT5G64120" "AT3G07390" "AT2G19880" "AT1G78290" "AT1G12520"
## [295] "AT4G08360" "AT5G03995" "AT4G32800" "AT4G32940" "AT4G12290" "AT1G33612"
## [301] "AT4G07820" "AT3G61680" "AT5G65200" "AT2G04090" "AT3G09220" "AT2G39890"
## [307] "AT4G34500" "AT2G38940" "AT3G04480" "AT4G23010" "AT2G27000" "AT2G28250"
## [313] "AT4G33030" "AT5G24410" "AT1G60680" "AT3G26450" "AT3G47210" "AT3G63270"
## [319] "AT2G18450" "AT2G01670" "AT3G51560" "AT2G27550" "AT4G21250" "AT2G38400"
## [325] "AT4G25310" "AT5G02800" "AT1G16420" "AT3G61260" "AT3G26330" "AT4G17100"
## [331] "AT1G56360" "AT4G39640" "AT4G26010" "AT2G37780" "AT2G42980" "AT5G44610"
## [337] "AT4G23070" "AT5G65687" "AT2G25410" "AT1G29179" "AT2G22240" "AT4G01970"
## [343] "AT5G52260" "AT1G44050" "AT5G43300" "AT3G01810" "AT5G53820" "AT3G62280"
## [349] "AT2G25000" "AT1G72360" "AT3G02620" "AT1G51850" "AT2G46860" "AT3G22800"
## [355] "AT5G44020" "AT5G63600" "AT2G40150" "AT3G49370" "AT3G04370" "AT4G20780"
## [361] "AT2G45220" "AT5G65040" "AT2G42060" "AT5G63410" "AT5G43370" "AT5G45500"
## [367] "AT2G34070" "AT2G26640" "AT1G79030" "AT5G39430" "AT3G45440" "AT2G21045"
## [373] "AT5G01560" "AT1G16160" "AT5G07220" "AT5G09220" "AT5G46780" "AT3G47220"
## [379] "AT1G25530" "AT4G37340" "AT3G19553" "AT1G68150" "AT4G30080" "AT4G32790"
## [385] "AT4G02410" "AT5G04680" "AT4G18950" "AT1G24320" "AT1G77690" "AT1G72220"
## [391] "AT5G06510" "AT2G23620" "AT1G61930" "AT1G29280" "AT1G12940" "AT5G64100"
## [397] "AT3G05320" "AT2G18640" "AT3G16690" "AT5G11790" "AT2G30540" "AT5G63570"
## [403] "AT1G44020" "AT3G50470" "AT1G68470" "AT1G47480" "AT3G28345" "AT5G60300"
## [409] "AT3G10300" "AT1G05850" "AT5G15860" "AT1G34750" "AT4G26790" "AT4G11230"
## [415] "AT1G05810" "AT5G46790" "AT3G62960" "AT5G18500" "AT5G60920" "AT4G12730"
## [421] "AT2G44490" "AT1G10020" "AT2G43120" "AT1G66440" "AT3G20935" "AT3G05860"
## [427] "AT1G64400" "AT1G14080" "AT5G53110" "AT1G25580" "AT3G44940" "AT1G56520"
## [433] "AT3G18460" "AT4G11530" "AT1G30900" "AT4G28850" "AT2G18650" "AT5G07150"
## [439] "AT1G23140" "AT4G04930" "AT3G12240" "AT5G07475" "AT4G10530" "AT5G45440"
## [445] "AT1G61740" "AT3G02140" "AT5G36870" "AT4G21400" "AT3G58000" "AT5G04150"
## [451] "AT1G34200" "AT2G25240" "AT5G41700" "AT4G36570" "AT4G01700" "AT2G35730"
## [457] "AT5G25640" "AT4G16400" "AT1G44608" "AT5G40510" "AT1G10550" "AT2G03360"
## [463] "AT1G28310" "AT5G47950" "AT5G23510" "AT5G66595" "AT2G32390" "AT4G35900"
## [469] "AT2G43220" "AT1G77530" "AT5G25050" "AT1G62262" "AT5G53160" "AT3G60720"
## [475] "AT5G07780" "AT4G02630" "AT1G73330" "AT5G20410" "AT1G47740" "AT5G41590"
## [481] "AT1G22740" "AT5G67430" "AT1G55390" "AT5G45490" "AT4G37430" "AT1G13640"
## [487] "AT1G67110" "AT2G18730" "AT4G20700" "AT4G21410" "AT3G20850" "AT3G29034"
## [493] "AT1G13970" "AT5G09480" "AT5G13810" "AT5G37420" "AT1G64780" "AT1G02575"
## [499] "AT5G19770" "AT1G27420" "AT2G21650" "AT2G04430" "AT5G07070" "AT5G60770"
## [505] "AT1G74210" "AT5G44910" "AT1G28170" "AT4G02330" "AT1G52420" "AT2G44581"
## [511] "AT1G65310" "AT5G45340" "AT3G51330" "AT1G27960" "AT1G33870" "AT4G07960"
## [517] "AT3G20340" "AT5G56300" "AT4G25970" "AT2G35612" "AT3G50620" "AT3G63280"
## [523] "AT1G18330" "AT1G10350" "AT5G43420" "AT3G13480" "AT5G36250" "AT4G25090"
## [529] "AT5G46140" "AT2G17700" "AT5G09735" "AT3G61440" "AT2G31020" "AT1G02360"
## [535] "AT3G57740" "AT3G07010" "AT3G03260" "AT5G19930" "AT2G42140" "AT3G59930"
## [541] "AT4G23000" "AT4G13770" "AT3G07570" "AT1G24620" "AT5G14340" "AT1G74940"
## [547] "AT2G32295" "AT3G50460" "AT5G06390" "AT4G21960" "AT1G75360" "AT5G52710"
## [553] "AT5G61290" "AT2G36630" "AT4G02270" "AT5G04840" "AT4G25160" "AT4G25030"
## [559] "AT1G08930" "AT3G14610" "AT3G01870" "AT2G03450" "AT3G43600" "AT1G75680"
## [565] "AT4G00300" "AT1G72430" "AT2G44160" "AT5G67400" "AT5G66420" "AT2G04410"
## [571] "AT1G77525" "AT1G21360" "AT5G37600" "AT2G46660" "AT3G17440" "AT3G46330"
## [577] "AT5G17820" "AT5G63910" "AT4G12360" "AT5G61570" "AT5G45480" "AT1G51940"
## [583] "AT3G28050" "AT1G60110" "AT1G77145" "AT3G07340" "AT2G40540" "AT5G23810"
## [589] "AT2G39410" "AT3G02250" "AT1G43650" "AT1G70900" "AT1G33170" "AT3G18170"
## [595] "AT4G11820" "AT2G02800" "AT5G24180" "AT3G15510" "AT3G48840" "AT5G43170"
## [601] "AT1G60095" "AT5G06610" "AT4G31550" "AT1G11580" "AT3G09940" "AT5G59450"
## [607] "AT3G02290" "AT3G62210" "AT3G29360" "AT5G04470" "AT4G08040" "AT3G50560"
## [613] "AT5G10820" "AT3G47000" "AT5G45370" "AT5G64500" "AT3G16180" "AT3G46720"
## [619] "AT3G27190" "AT4G06195" "AT3G48346" "AT2G03730" "AT3G21260" "AT1G03445"
## [625] "at3g59884" "AT2G19160" "AT4G15360" "AT3G06145" "AT4G15350" "AT5G09470"
## [631] "AT3G01690" "AT2G43200" "AT4G25070" "AT1G80050" "AT5G20640" "AT5G58780"
## [637] "AT2G23990" "AT2G44340" "AT2G35880" "AT2G32260" "AT4G23060" "AT3G14470"
## [643] "AT4G12450" "AT3G18780" "AT1G53635" "AT4G24240" "AT5G37690" "AT1G26200"
## [649] "AT3G62390" "AT1G11680" "AT1G16750" "AT3G51670" "AT1G09400" "AT1G30910"
## [655] "AT4G35920" "AT1G76430" "AT1G72160" "AT3G23870" "AT4G33770" "AT1G76160"
## [661] "AT2G19050" "AT1G01430" "AT5G36940" "AT1G53233" "AT2G35930" "AT4G03460"
## [667] "AT1G56160" "AT1G70110" "AT1G52200" "AT2G42320" "AT1G63550" "AT2G43020"
## [673] "AT5G56340" "AT5G17590" "AT4G01720" "AT1G58330" "AT2G38120" "AT3G58190"
## [679] "AT4G27430" "AT4G16490" "AT1G31420" "AT1G03210" "AT1G05990" "AT4G30910"
## [685] "AT5G42010" "AT1G34670" "AT3G53840" "AT5G66920" "AT3G02885" "AT1G22280"
## [691] "AT2G28850" "AT4G16600" "AT3G25030" "AT2G04190" "AT5G06930" "AT5G48780"
## [697] "AT1G49390" "AT5G01840" "AT1G65840" "AT2G36570" "AT5G40230" "AT5G43540"
## [703] "AT5G23360" "AT4G14980" "AT5G07240" "AT5G58900" "AT5G02230" "AT1G19920"
## [709] "AT2G01900" "AT4G37850" "AT3G25930" "AT2G13900" "AT1G12290" "AT5G44690"
## [715] "AT2G45360" "AT5G58560" "AT1G64405" "AT1G03970" "AT1G31885" "AT5G61340"
## [721] "AT3G26820" "AT3G02870" "AT2G30070" "AT1G66800" "AT1G47603" "AT4G11090"
## [727] "AT5G43920" "AT5G25240" "AT3G49050" "AT2G38630" "AT4G04700" "AT4G10390"
## [733] "AT1G13710" "AT2G25220" "AT5G05170" "AT5G59700" "AT5G25250" "AT5G33280"
## [739] "AT2G38320" "AT5G65683" "AT5G01040" "AT4G24310" "AT1G49570" "AT2G46530"
## [745] "AT2G29670" "AT4G33120" "AT5G19080" "AT2G05260" "AT3G47420" "AT4G37400"
## [751] "AT1G19360" "AT5G33290" "AT1G69690" "AT5G45840" "AT1G34050" "AT2G45890"
## [757] "AT1G29020" "AT1G61950" "AT2G13950" "AT3G02630" "AT1G22882" "AT4G30640"
## [763] "AT3G03760" "AT2G26040" "AT1G13500" "AT1G48300" "AT3G29400" "AT1G63500"
## [769] "AT3G20380" "AT3G23410" "AT3G26935" "AT5G46540" "AT1G49240" "AT1G05660"
## [775] "AT5G26660" "AT4G23980" "AT1G29230" "AT2G23530" "AT3G05690" "AT3G23340"
## [781] "AT3G47380" "AT1G07620" "AT2G28120" "AT3G23190" "AT1G59780" "AT5G26280"
## [787] "AT5G14480" "AT2G34000" "AT1G55120" "AT2G41240" "AT1G12090" "AT4G00550"
## [793] "AT1G30110" "AT4G13510" "AT5G11540" "AT5G67190" "AT3G14370" "AT3G02880"
## [799] "AT2G46890" "AT5G49720" "AT4G14570" "AT3G58620" "AT1G13440" "AT5G03040"
## [805] "AT4G20460" "AT1G01448" "AT1G67560" "AT1G15600" "AT3G26700" "AT3G09790"
## [811] "AT3G13760" "AT5G39000" "AT2G01570" "AT3G08600" "AT1G23030" "AT1G14600"
## [817] "AT1G58100" "AT4G11290" "AT1G28340" "AT1G79760" "AT5G08750" "AT2G44500"
## [823] "AT2G28930" "AT3G63080" "AT2G45590" "AT1G13420" "AT4G25300" "AT4G35310"
## [829] "AT3G02240" "AT1G55365" "AT5G28010" "AT5G64410" "AT1G54000" "AT3G20540"
## [835] "AT5G18670" "AT1G20260" "AT1G05700" "AT1G01300" "AT2G26410" "AT2G03090"
## [841] "AT1G59960" "AT1G48640" "AT3G60320" "AT4G21230" "AT1G01750" "AT1G72880"
## [847] "AT2G20562" "AT2G34470" "AT2G33710" "AT1G33780" "AT1G70450" "AT4G16110"
## [853] "AT2G39740" "AT5G05840" "AT1G47670" "AT1G69810" "AT2G03720" "AT1G50580"
## [859] "AT5G13820" "AT5G24880" "AT2G43910" "AT1G77420" "AT5G48770" "AT2G30930"
## [865] "AT5G05460" "AT4G12520" "AT5G37250" "AT4G25230" "AT2G45720" "AT5G26320"
## [871] "AT1G19900" "AT5G64550" "AT1G65560" "AT3G07270" "AT5G52670" "AT1G10400"
## [877] "AT1G67270" "AT3G13437" "AT1G53310" "AT2G42490" "AT1G56720" "AT1G59580"
## [883] "AT1G79410" "AT4G01140" "AT1G04040" "AT3G48080" "AT1G51480" "AT3G05490"
## [889] "AT5G41140" "AT3G46240" "AT4G10550" "AT2G43620" "AT4G03330" "AT5G01050"
## [895] "AT5G22050" "AT1G74460" "AT5G26780" "AT3G21510" "AT5G60310" "AT1G01440"
## [901] "AT1G65590" "AT2G45510" "AT1G17040" "AT4G40050" "AT3G63260" "AT5G63990"
## [907] "AT2G23790" "AT5G13760" "AT3G20360" "AT3G06150" "AT1G06120" "AT2G30100"
## [913] "AT4G04340" "AT1G66110" "AT1G69340" "AT2G23810" "AT3G60550" "AT2G46710"
## [919] "AT4G11300" "AT3G59130" "AT4G22756" "AT5G14920" "AT4G22640" "AT5G44585"
## [925] "AT1G04010" "AT3G44820" "AT5G41260" "AT2G31310" "AT4G36220" "AT3G59730"
## [931] "AT1G51630" "AT1G80870" "AT1G09430" "AT5G56660" "AT1G19110" "AT3G02750"
## [937] "AT4G15210" "AT1G01640" "AT5G16530" "AT1G19000" "AT1G69580" "AT5G60280"
## [943] "AT5G14330" "AT5G02200" "AT3G43890" "AT3G05150" "AT1G73310" "AT4G03940"
## [949] "AT2G30490" "AT5G12200" "AT4G02860" "AT5G14200" "AT5G44920" "AT5G10410"
## [955] "AT4G15417" "AT4G29740" "AT1G55535" "AT1G52660" "AT1G08650" "AT2G23780"
## [961] "AT4G33020" "AT1G09023" "AT3G27390" "AT5G08170" "AT5G65158" "AT3G23430"
## [967] "AT1G22410" "AT3G57510" "AT4G24170" "AT4G21390" "AT4G30520" "AT1G16150"
## [973] "AT2G35840" "AT1G06830" "AT1G55430" "AT2G19970" "AT1G02810" "AT2G44110"
## [979] "AT1G14350" "AT2G26660" "AT1G29830" "AT5G55730" "AT5G45120" "AT5G10965"
## [985] "AT2G38290" "AT3G27610" "AT1G33610" "AT1G01180" "AT1G04837" "AT2G25200"
## [991] "AT5G16590" "AT5G17680" "AT5G02400" "AT2G44790" "AT3G11820" "AT4G13930"
## [997] "AT2G10930" "AT3G32980" "AT1G22070" "AT3G14020" "AT3G45210" "AT1G34760"
## [1003] "AT4G23650" "AT2G44380" "AT3G08510" "AT5G01330" "AT1G65960" "AT4G33080"
## [1009] "AT2G36320" "AT4G36790" "AT1G30730" "AT5G44340" "AT1G06620" "AT5G15330"
## [1015] "AT4G28260" "AT1G11130" "AT5G10280" "AT4G31170" "AT3G03910" "AT3G04360"
## [1021] "AT3G63350" "AT1G70370" "AT5G54780" "AT1G79590" "AT5G45220" "AT4G29610"
## [1027] "AT1G56280" "AT1G34520" "AT2G28840" "AT3G02860" "AT3G57650" "AT5G49820"
## [1033] "AT3G46830" "AT5G42280" "AT5G22360" "AT2G42580" "AT4G00500" "AT1G20560"
## [1039] "AT5G40250" "AT4G30440" "AT3G02430" "AT3G07490" "AT5G43350" "AT4G23870"
## [1045] "AT5G40240" "AT3G50710" "AT5G44130" "AT3G58490" "AT3G50060" "AT5G10430"
## [1051] "AT4G24890" "AT3G57420" "AT2G47370" "AT5G09690" "AT5G38340" "AT5G03520"
## [1057] "AT5G27450" "AT3G52400" "at2g34202" "AT2G36310" "AT5G02360" "AT1G10155"
## [1063] "AT3G45650" "AT5G39490" "AT4G35320" "AT1G58070" "AT4G34580" "AT3G10210"
## [1069] "AT4G24100" "AT4G10840" "AT4G20362" "AT2G45910" "AT5G58700" "AT5G15130"
## [1075] "AT1G02290" "AT4G34950" "AT2G33775" "AT1G11920" "AT4G32420" "AT4G14290"
## [1081] "AT2G28890" "AT1G44160" "AT5G23280" "AT1G70990" "AT3G23820" "AT4G15540"
## [1087] "AT1G07520" "AT4G08770" "AT3G29180" "AT2G17050" "AT5G02580" "AT3G19970"
## [1093] "AT1G71692" "AT1G80730" "AT5G19230" "AT4G12420" "AT4G22230" "AT1G71015"
## [1099] "AT3G50300" "AT1G76220" "AT4G14365" "AT2G16380" "AT5G59930" "AT3G09290"
## [1105] "AT5G49870" "AT1G57570" "AT5G57940" "AT2G02640" "AT2G21540" "AT1G67940"
## [1111] "AT3G03000" "AT4G28270" "AT1G55440" "AT5G44480" "AT3G59680" "AT5G56610"
## [1117] "AT1G25510" "AT1G60390" "AT1G77280" "AT1G03840" "AT5G26010" "AT4G00680"
## [1123] "AT5G58860" "AT3G42180" "AT4G11320" "AT4G39950" "AT1G72950" "AT3G27630"
## [1129] "AT5G60660" "AT4G22580" "AT3G59690" "AT4G27852" "AT3G15300" "AT2G26510"
## [1135] "AT4G32650" "AT5G24655" "AT2G14510" "AT5G54160" "AT1G23980" "AT1G78530"
## [1141] "AT1G55450" "AT1G29740" "AT5G08260" "AT1G64070" "AT5G01520" "AT5G16190"
## [1147] "AT5G59020" "AT3G17650" "AT4G04450" "AT1G65730" "AT3G18215" "AT4G15300"
## [1153] "AT2G28970" "AT5G64740" "AT3G12020" "AT1G18670" "AT5G60490" "AT1G67328"
## [1159] "AT2G37280" "AT5G55960" "AT2G44280" "AT3G13360" "AT1G17060" "AT1G15125"
## [1165] "AT2G44210" "AT3G01760" "AT3G59760" "AT1G02980" "AT3G21770" "AT1G34060"
## [1171] "AT2G36330" "AT4G06536" "AT5G01060" "AT4G32020" "AT5G15290" "AT3G01720"
## [1177] "AT3G01930" "AT5G17090" "AT5G40440" "AT2G29740" "AT1G79420" "AT3G52370"
## [1183] "AT2G39518" "AT5G26720"# downregulated genes
v2 <- list("leaf 3d dn"=del3_dn, "leaf 5d dn"=del5_dn,
"root 3d dn" =der3_dn , "root 5d dn"=der5_dn)
plot(euler(v2),quantities = TRUE)
intersect(del3_dn,del5_dn)## [1] "AT4G02720" "AT4G23680" "AT1G19840" "AT3G62130" "AT1G19600" "AT1G17180"
## [7] "AT2G32190" "AT3G16770" "AT5G17330" "AT1G34180" "AT4G28720" "AT3G16420"
## [13] "AT5G62150" "AT2G33840" "AT5G50760" "AT3G62730" "AT5G26731" "AT1G53830"
## [19] "AT1G49000" "AT4G30180" "AT2G27830" "AT4G30190" "AT5G46240" "AT1G68500"
## [25] "AT2G05510" "AT2G47560" "AT1G16120" "AT1G18970" "AT3G22240" "AT4G30960"
## [31] "AT4G29700" "AT4G13420" "AT3G49570" "AT2G02230" "AT3G62270" "AT1G70170"
## [37] "AT1G20990" "AT1G23150" "AT3G62830" "AT1G77400" "AT5G07570" "AT1G05000"
## [43] "AT1G65690" "AT4G33960" "AT3G09400" "AT2G47870" "AT3G05880" "AT3G52450"
## [49] "AT5G47550" "AT5G13900" "AT4G19200" "AT1G77180" "AT4G35720" "AT2G42360"
## [55] "AT5G66170" "AT5G19410" "AT5G43980" "AT5G47590" "AT4G39190" "AT4G30670"
## [61] "AT4G18280" "AT4G14819" "AT4G29340" "AT3G60520" "AT1G64370" "AT2G23150"
## [67] "AT3G23325" "AT1G01190" "AT2G39700" "AT5G64260" "AT5G14000" "AT5G14730"
## [73] "AT2G18480" "AT4G21990" "AT2G31200" "AT3G15150" "AT1G19830" "AT1G77760"
## [79] "AT5G58570" "AT5G12930" "AT3G19030" "AT1G70300" "AT2G02120" "AT3G49940"
## [85] "AT2G47485" "AT5G39590" "AT1G64170" "AT1G77590" "AT5G51200" "AT4G23860"
## [91] "AT1G18980" "AT2G02010" "AT2G36270" "AT3G58930" "AT4G17215" "AT1G07780"
## [97] "AT3G26140" "AT5G65010" "AT5G59990" "AT3G60330" "AT2G35820" "AT1G62480"
## [103] "AT1G22500" "AT4G14630" "AT5G40670" "AT5G45350" "AT5G22890" "AT3G50770"
## [109] "AT5G11100" "AT5G12940" "AT1G62422" "AT1G56320" "AT2G31980" "AT5G19970"
## [115] "AT1G30560" "AT2G37570" "AT1G03820" "AT5G06210" "AT4G34881" "AT3G07350"
## [121] "AT4G04830" "AT2G37330" "AT1G60450" "AT4G18550" "AT2G16760" "AT3G18140"
## [127] "AT1G23730" "AT1G12110" "AT3G52748" "AT5G57567" "AT5G40010" "AT4G33740"
## [133] "AT3G05200" "AT1G70800" "AT2G38170" "AT4G39300" "AT5G18290" "AT5G10580"
## [139] "AT1G21550" "AT5G12140" "AT5G66658" "AT1G13480" "AT4G17340" "AT3G61630"
## [145] "AT2G34690" "AT1G78400" "AT1G66180" "AT1G19190" "AT2G45280" "AT1G68620"
## [151] "AT3G55646" "AT4G20820" "AT5G07440" "AT1G44750" "AT5G09520" "AT5G55190"
## [157] "AT3G27025" "AT5G66650" "AT5G01180" "AT2G39350" "AT5G47530" "AT3G62990"
## [163] "AT5G62490" "AT1G14870" "AT1G53170" "AT1G20190" "AT4G29820" "AT1G36370"
## [169] "AT1G48750" "AT1G28400" "AT4G24420" "AT3G49580" "AT4G05200" "AT4G03540"
## [175] "AT1G55240" "AT5G57350" "AT1G24575" "AT3G56130" "AT5G61890" "AT3G07870"
## [181] "AT3G18560" "AT4G21110" "AT1G20693" "AT5G41590" "AT1G12030" "AT4G23670"
## [187] "AT3G03650" "AT4G31140" "AT1G51830" "AT4G20320" "AT5G28520" "AT2G23120"
## [193] "AT2G30360" "AT4G39675" "AT2G06040" "AT2G18160" "AT2G23540" "AT2G37170"
## [199] "AT1G66173" "AT5G02480" "AT2G41800" "AT4G01360" "AT1G66830" "AT1G32928"
## [205] "AT5G13580" "AT3G46190" "AT1G68350" "AT2G17840" "AT1G78650" "AT2G02955"
## [211] "AT3G30725" "AT4G14030" "AT3G22910" "AT1G49840" "AT5G06090" "AT1G70670"
## [217] "AT5G38200" "AT4G31910" "AT5G47130" "AT3G08030" "AT1G60610" "AT5G37740"
## [223] "AT1G09870" "AT5G09530" "AT2G36930" "AT4G24130" "AT5G42980" "AT1G31750"
## [229] "AT2G35770" "AT3G50400" "AT3G16730" "AT2G40400" "AT4G11070" "AT1G54540"
## [235] "AT4G18630" "AT3G29575" "AT2G37440" "AT4G28703" "AT4G21650" "AT4G17280"
## [241] "AT3G01200" "AT5G46370" "AT5G11090" "AT5G40460" "AT1G61480" "AT5G15960"
## [247] "AT5G26146" "AT3G56240" "AT4G31330" "AT5G22310" "AT3G44550" "AT2G23070"
## [253] "AT1G62420" "AT3G12520" "AT1G70690" "AT4G15960" "AT1G52980" "AT1G45145"
## [259] "AT1G75440" "AT2G41200" "AT1G75390" "AT4G35640" "AT2G15620" "AT5G19600"
## [265] "AT5G02260" "AT1G18870" "AT1G26450" "AT5G62680" "AT3G49760" "AT1G27200"
## [271] "AT1G15310" "AT3G22600" "AT2G41410" "AT5G46140" "AT4G28230" "AT2G39800"
## [277] "AT2G22080" "AT3G21710" "AT1G59660" "AT1G74000" "AT4G32920" "AT5G53700"
## [283] "AT1G75280" "AT5G37980" "AT1G51340" "AT2G01580" "AT1G19230" "AT3G03341"
## [289] "AT3G59850" "AT5G52390" "AT1G27670" "AT4G25670" "AT3G48510" "AT3G09270"
## [295] "AT2G41480" "AT1G04770" "AT2G18340" "AT3G56200" "AT3G50260" "AT5G63030"
## [301] "AT1G64140" "AT2G42350" "AT2G47200" "AT3G21480" "AT3G61900" "AT1G02400"
## [307] "AT4G32480" "AT3G05165" "AT1G66530" "AT1G05450" "AT1G65220" "AT5G49350"
## [313] "AT1G70440" "AT1G28815" "AT2G25690" "AT3G14560" "AT1G69252"intersect(der3_dn,der3_dn)## [1] "AT5G38910" "AT4G19810" "AT5G39100" "AT2G46750" "AT2G26695" "AT3G49570"
## [7] "AT3G49580" "AT4G34710" "AT5G39110" "AT5G19600" "AT5G39120" "AT2G13810"
## [13] "AT2G43590" "AT5G48850" "AT2G20180" "AT2G27120" "AT4G31330" "AT4G02360"
## [19] "AT5G64810" "AT2G26560" "AT4G10500" "AT1G05340" "AT2G18480" "AT1G18100"
## [25] "AT2G26700" "AT2G02120" "AT4G23680" "AT5G06860" "AT1G19960" "AT1G04770"
## [31] "AT5G39150" "AT4G04830" "AT3G08860" "AT2G04050" "AT3G62040" "AT3G16530"
## [37] "AT1G62710" "AT5G28520" "AT1G36370" "AT4G01870" "AT5G24030" "AT3G51895"
## [43] "AT1G01190" "AT2G04070" "AT4G21990" "AT5G38200" "AT3G11930" "AT5G57350"
## [49] "AT3G12520" "AT3G12700" "AT1G01140" "AT5G18170" "AT4G11650" "AT2G24260"
## [55] "AT3G05400" "AT3G62730" "AT1G17840" "AT1G66180" "AT1G68620" "AT1G08763"
## [61] "AT1G15380" "AT1G15830" "AT4G12580" "AT1G71050" "AT2G43570" "AT5G28510"
## [67] "AT5G06730" "AT3G15500" "AT1G51340" "AT2G18660" "AT5G13080" "AT4G33666"
## [73] "AT3G13433" "AT4G18350" "AT5G22390" "AT5G59540" "AT1G20180" "AT3G04070"
## [79] "AT1G60470" "AT5G10180" "AT1G08430" "AT4G19760" "AT1G48750" "AT1G29670"
## [85] "AT1G51330" "AT4G09120" "AT3G47580" "AT4G15490" "AT3G47480" "AT2G47560"
## [91] "AT1G78000" "AT2G37330" "AT5G59220" "AT1G24130" "AT2G32487" "AT1G08697"
## [97] "AT4G14630" "AT3G14990" "AT3G52970" "AT1G06493" "AT5G07050" "AT2G46680"
## [103] "AT4G30960" "AT2G45135" "AT5G64210" "AT3G61890" "AT1G15825" "AT4G13420"
## [109] "AT3G30210" "AT5G12930" "AT5G40010" "AT3G25882" "AT1G70830" "AT4G19700"
## [115] "AT1G09080" "AT4G35640" "AT1G74590" "AT1G75900" "AT5G07560" "AT3G24310"
## [121] "AT2G43510" "AT5G63350" "AT5G24640" "AT3G50970" "AT2G40460" "AT4G21200"
## [127] "AT4G25700" "AT1G22900" "AT2G36780" "AT5G59320" "AT1G65690" "AT4G04570"
## [133] "AT2G17640" "AT1G66760" "AT1G02310" "AT3G49120" "AT4G00070" "AT1G18870"
## [139] "AT1G22430" "AT4G19750" "AT4G36880" "AT5G13330" "AT4G33070" "AT2G25690"
## [145] "AT5G39520" "AT3G62990" "AT5G66650" "AT5G14780" "AT2G15220" "AT5G24660"
## [151] "AT5G01300" "AT1G45201" "AT3G48510" "AT2G32510" "AT1G17615" "AT4G17340"
## [157] "AT3G28510" "AT4G37050" "AT3G21090" "AT1G51500" "AT5G64250" "AT3G60415"
## [163] "AT1G13520" "AT4G13250" "AT2G16005" "AT3G06210" "AT1G74010" "AT5G13170"
## [169] "AT1G02920" "AT2G39450" "AT5G67340" "AT4G19740" "AT3G45730" "AT3G55090"
## [175] "AT1G72970" "AT1G28010" "AT5G11210" "AT4G37370" "AT5G13320" "AT4G38810"
## [181] "AT2G44460" "AT5G50260" "AT2G16890" "AT2G30140" "AT3G55790" "AT2G23150"
## [187] "AT3G16330" "AT1G73260" "AT4G33550" "AT5G01720" "AT1G52890" "AT5G23050"
## [193] "AT1G07720" "AT1G68880" "AT1G02205" "AT5G47050" "AT5G47240" "AT5G06905"
## [199] "AT4G27410" "AT5G50360" "AT5G26340" "AT3G22740" "AT1G26450" "AT2G34610"
## [205] "AT4G19230" "AT5G47450" "AT1G24600" "AT1G74458" "AT1G27200" "AT2G43000"
## [211] "AT2G39800" "AT5G62350" "AT1G31050" "AT2G38540" "AT4G13480" "AT1G22640"
## [217] "AT5G26220" "AT1G05560" "AT4G25960" "AT2G29380" "AT1G71140" "AT2G28270"
## [223] "AT4G31140" "AT2G41190" "AT4G32210" "AT5G06865" "AT3G53470" "AT4G03420"
## [229] "AT1G07430" "AT1G73810" "AT2G36640" "AT2G36270" "AT1G73390" "AT3G20470"
## [235] "AT1G56600" "AT5G11650" "AT4G24510" "AT1G44180" "AT3G46650" "AT3G11410"
## [241] "AT1G70440" "AT4G37870" "AT4G05380" "AT4G12430" "AT1G32870" "AT3G28320"
## [247] "AT4G35190" "AT1G76470" "AT4G10860" "AT5G61820" "AT3G57540" "AT1G49200"
## [253] "AT1G15310" "AT4G23700" "AT5G62530" "AT4G19200" "AT2G31980" "AT1G77450"
## [259] "AT1G26410" "AT4G39330" "AT5G02480" "AT1G70640" "AT1G77760" "AT3G16370"
## [265] "AT2G30750" "AT1G56580" "AT5G22500" "AT2G39490" "AT3G55310" "AT4G33220"
## [271] "AT1G19750" "AT5G43580" "AT3G28290" "AT3G28300" "AT3G22370" "AT1G55240"
## [277] "AT4G30460" "AT3G46190" "AT1G69260" "AT4G37060" "AT1G32940" "AT5G53700"
## [283] "AT4G15550" "AT4G28703" "AT5G66260" "AT4G16220" "AT5G24220" "AT5G45950"
## [289] "AT1G80820" "AT1G09180" "AT3G56400" "AT3G19100" "AT1G78230" "AT1G36622"
## [295] "AT3G50260" "AT1G04180" "AT5G25460" "AT1G02230" "AT4G24010" "AT4G28840"
## [301] "AT3G09390" "AT5G41740" "AT5G06320" "AT4G30270" "AT3G56240" "AT5G27350"
## [307] "AT2G35300" "AT5G17460" "AT4G34320" "AT4G23860" "AT1G12110" "AT1G73805"
## [313] "AT1G73880" "AT3G57260" "AT3G02480" "AT5G17650" "AT2G38823" "AT3G48850"
## [319] "AT5G50760" "AT1G75210" "AT3G08870" "AT3G48520" "AT5G61650" "AT5G39090"
## [325] "AT4G29340" "AT5G24080" "AT1G68530" "AT4G04610" "AT5G15960" "AT3G01970"
## [331] "AT4G25860" "AT5G39030" "AT1G62280" "AT1G16850" "AT2G29460" "AT1G07900"
## [337] "AT3G22550" "AT3G23450" "AT1G04560" "AT1G46768" "AT4G33467" "AT3G22830"
## [343] "AT4G00305" "AT4G28040" "AT2G24180" "AT3G61630" "AT5G66400" "AT5G07010"
## [349] "AT1G70740" "AT2G42250" "AT5G43840" "AT4G21750" "AT3G62090" "AT4G28490"
## [355] "AT4G16146" "AT2G05510" "AT5G43180" "AT5G11090" "AT1G68020" "AT2G16720"
## [361] "AT1G02850" "AT5G18470" "AT4G21440" "AT5G58330" "AT4G00430" "AT1G13480"
## [367] "AT5G17430" "AT4G23880" "AT1G68500" "AT5G65790" "AT1G78850" "AT3G14690"
## [373] "AT2G02060" "AT3G27250" "AT5G59520" "AT4G31830" "AT5G44567" "AT2G32660"
## [379] "AT5G14550" "AT1G32350" "AT4G12735" "AT4G37730" "AT4G04490" "AT1G07400"
## [385] "AT4G36040" "AT5G53990" "AT1G53625" "AT3G05165" "AT3G12910" "AT4G30470"
## [391] "AT5G38980" "AT5G13370" "AT2G07335" "AT2G37870" "AT4G26120" "AT5G39190"
## [397] "AT3G52720" "AT4G34250" "AT4G37790" "AT4G26080" "AT1G53470" "AT3G14440"
## [403] "AT1G57943" "AT2G31945" "AT3G47600" "AT4G17740" "AT5G54165" "AT1G69526"
## [409] "AT5G24380" "AT1G53170" "AT2G41730" "AT1G12200" "AT1G05330" "AT1G19850"
## [415] "AT3G57160" "AT1G49470" "AT5G52310" "AT1G26420" "AT3G22240" "AT2G27830"
## [421] "AT5G52320" "AT1G69572" "AT4G33905" "AT1G80770" "AT4G15260" "AT5G04370"
## [427] "AT5G38900" "AT4G33420" "AT2G31070" "AT1G77920" "AT1G73930" "AT4G23920"
## [433] "AT4G28460" "AT4G20820" "AT4G32540" "AT2G42840" "AT1G17020" "AT2G15580"
## [439] "AT3G25710" "AT1G01720" "AT4G32380" "AT2G26690" "AT5G49138" "AT2G25625"
## [445] "AT3G57830" "AT3G27820" "AT1G05100" "AT3G22100" "AT5G17760" "AT5G03210"
## [451] "AT2G15490" "AT1G69120" "AT5G57660" "AT5G13400" "AT2G37760" "AT1G12030"
## [457] "AT2G16700" "AT4G22070" "AT1G77990" "AT5G23660" "AT5G52570" "AT4G12350"
## [463] "AT2G38530" "AT2G23170" "AT5G42900" "AT3G49130" "AT5G17850" "AT2G47020"
## [469] "AT1G80110" "AT2G40390" "AT3G03660" "AT1G52000" "AT1G05383" "AT3G28007"
## [475] "AT4G17470" "AT3G18440" "AT3G11660" "AT5G48400" "AT2G21130" "AT4G37150"
## [481] "AT4G11655" "AT5G39050" "AT1G06130" "AT3G63060" "AT4G28410" "AT2G30580"
## [487] "AT3G01500" "AT3G20300" "AT5G52550" "AT5G59310" "AT5G59190" "AT3G10430"
## [493] "AT3G46230" "AT2G30310" "AT5G05410" "AT1G78950" "AT3G26460" "AT1G79470"
## [499] "AT1G11300" "AT2G01020" "AT3G41979" "AT5G02020" "AT2G38920" "AT3G08590"
## [505] "AT4G25850" "AT1G54100" "AT1G55110" "AT2G41480" "ATCG01020" "AT5G14570"
## [511] "AT1G26390" "AT5G06760" "AT1G05680" "AT3G17520" "AT1G64110" "AT2G16060"
## [517] "AT3G62270" "AT2G23120" "AT2G30670" "AT5G19855" "AT1G04778" "AT3G50030"
## [523] "AT4G08250" "AT3G21352" "AT4G16233" "AT4G11910" "AT3G29575" "AT4G25670"
## [529] "AT5G43980" "AT3G60520" "AT1G52827" "AT3G27690" "AT4G31520" "AT1G52400"
## [535] "AT4G35480" "AT5G53970" "AT2G31280" "AT1G62580" "AT1G58300" "AT5G57050"
## [541] "AT5G39610" "AT5G26146" "AT4G29050" "AT2G32690" "AT5G13490" "AT5G36700"
## [547] "AT5G22290" "AT1G55230" "AT3G63380" "AT3G56200" "AT5G06870" "AT2G47810"
## [553] "AT3G30725" "AT5G24770" "AT5G06900" "AT5G60850" "AT3G07365" "AT1G30620"
## [559] "AT5G18290" "AT1G54740" "AT2G33150" "AT4G21650" "AT3G62590" "AT1G14240"
## [565] "AT5G65710" "AT1G02770" "AT2G16630" "AT5G66480" "AT2G30500" "AT1G07470"
## [571] "AT1G47960" "AT1G60190" "AT1G64620" "AT2G25215" "AT1G66600" "AT5G62470"
## [577] "AT5G52720" "AT5G40370" "AT1G20450" "AT3G61450" "AT2G47770" "AT1G68750"
## [583] "AT2G03530" "AT5G38410" "AT4G23190" "AT3G05880" "AT4G13290" "AT1G35190"
## [589] "AT1G04500" "AT3G62690" "AT2G16500" "AT4G04620" "AT3G02100" "AT2G38240"
## [595] "AT1G64370" "AT1G54160" "AT5G52420" "AT4G09600" "AT5G47920" "AT5G49420"
## [601] "AT4G27460" "AT3G55730" "AT2G44480" "AT5G06530" "AT5G24160" "AT4G25900"
## [607] "AT1G53610" "AT2G32190" "AT3G13672" "AT1G05000" "AT2G02930" "AT3G21690"
## [613] "AT5G14940" "AT5G65990" "AT4G31290" "AT1G72770" "AT4G33740" "AT2G38250"
## [619] "AT5G59430" "AT2G42950" "AT1G08920" "AT1G70810" "AT1G64900" "AT2G36120"
## [625] "AT1G03790" "AT2G30360" "AT2G30770" "AT2G41870" "AT4G29020" "AT5G45630"
## [631] "AT5G09640" "AT4G08570" "AT1G78915" "AT2G42540" "AT2G21990" "AT2G20880"
## [637] "AT1G52690" "AT1G72760" "AT5G52390" "AT3G25870" "AT3G28910" "AT1G64670"
## [643] "AT1G17550" "AT1G29920" "AT3G13080" "AT4G37490" "AT5G59200" "AT1G66950"
## [649] "AT4G18280" "AT2G30550" "AT4G37030" "AT5G36970" "AT2G01430" "AT2G47950"
## [655] "AT5G54230" "AT3G52820" "AT3G23325" "AT3G62800" "AT2G39510" "AT3G02535"
## [661] "AT1G23730" "AT1G63750" "AT2G18050" "AT5G04250" "AT5G53710" "AT2G42247"
## [667] "AT5G25610" "AT4G10270" "AT4G21930" "AT2G46320" "AT3G26280" "AT4G21620"
## [673] "AT1G48405" "AT2G21640" "AT5G59570" "AT1G52790" "AT4G04890" "AT5G55135"
## [679] "AT2G41380" "AT1G01600" "AT2G01150" "AT4G25690" "AT5G37840" "AT5G23060"
## [685] "AT4G39190" "AT5G07440" "AT4G34680" "AT2G33380" "AT1G32080" "AT5G35735"
## [691] "AT1G74020" "AT4G22610" "AT1G79900" "AT5G22460" "AT5G05220" "AT1G11190"
## [697] "AT2G25297" "AT1G02660" "AT4G33560" "AT1G68320" "AT1G27950" "AT2G33080"
## [703] "AT5G39130" "AT3G04010" "AT2G41720" "AT2G47260" "AT3G58680" "AT2G39330"
## [709] "AT5G53730" "AT1G20070" "AT5G20350" "AT3G61550" "AT2G03760" "AT1G24575"
## [715] "AT2G20920" "AT1G69570" "AT1G62180" "AT1G17147" "AT5G26250" "AT5G03500"
## [721] "AT1G62290" "AT4G25434" "AT1G78170" "AT5G47560" "AT1G73480" "AT1G21890"
## [727] "AT2G40400" "AT2G43610" "AT1G07985" "AT1G80160" "AT1G50740" "AT5G57840"
## [733] "AT2G31083" "AT5G10770" "AT1G51090" "AT1G52820" "AT5G48480" "AT5G47600"
## [739] "AT1G06150" "AT1G27100" "AT3G63160" "AT5G57390" "AT1G69480" "AT1G48000"
## [745] "AT4G15760" "AT1G72740" "AT5G48175" "AT1G21670" "AT5G57785" "AT2G05540"
## [751] "AT3G53040" "AT3G27884" "AT1G52040" "AT5G53420" "AT1G69880" "AT3G06500"
## [757] "AT3G18250" "AT1G67148" "AT5G49740" "AT5G47800" "AT3G09400" "AT1G20440"
## [763] "AT1G10360" "AT2G26740" "AT3G50980" "AT1G63720" "AT5G22040" "AT1G62570"
## [769] "AT2G32830" "AT1G05160" "AT1G70420" "AT3G16210" "AT2G02390" "AT1G14870"
## [775] "AT3G52810" "AT1G08477" "AT5G12340" "AT2G17840" "AT2G48090" "AT5G07000"
## [781] "AT2G47600" "AT2G36950" "AT5G66130" "AT1G54260" "AT1G60950" "AT5G49700"
## [787] "AT1G33811" "AT1G78390" "AT1G21520" "AT5G37490" "AT2G47190" "AT5G22570"
## [793] "AT5G39590" "AT3G28920" "AT5G40670" "AT2G38830" "AT1G30700" "AT5G49665"
## [799] "AT5G01445" "AT4G06746" "AT1G35710" "AT2G23270" "AT3G16170" "AT2G46640"
## [805] "AT2G16990" "AT1G07180" "AT5G54170" "AT4G18980" "AT1G75270" "AT1G76680"
## [811] "AT5G40880" "AT4G01360" "AT2G39470" "AT3G22420" "AT3G23920" "AT4G20070"
## [817] "AT1G64170" "AT5G10300" "AT4G11370" "AT3G60470" "AT3G53400" "AT5G51750"
## [823] "AT1G75600" "AT4G18550" "AT4G39000" "AT5G08560" "AT5G48330" "AT1G49900"
## [829] "AT5G63790" "AT2G42720" "AT2G23030" "AT5G51440" "AT5G54250" "AT2G34430"
## [835] "AT3G18950" "AT2G44750" "AT3G05820" "AT4G02520" "AT1G28430" "AT1G09530"
## [841] "AT4G18170" "AT1G04710" "AT1G78610" "AT3G15670" "AT2G18360" "AT1G71080"
## [847] "AT4G34000" "AT5G41410" "AT5G54940" "AT3G51750" "AT5G25220" "AT4G11360"
## [853] "AT1G62620" "AT3G14770" "AT1G70880" "AT5G62480" "AT3G02990" "AT3G19090"
## [859] "AT4G23990" "AT5G28020" "AT5G65870" "AT5G11110" "AT1G72870" "AT5G01740"
## [865] "AT5G40405" "AT3G14420" "AT1G08280" "AT4G28390" "AT4G22240" "AT4G25380"
## [871] "AT1G62420" "AT1G25400" "AT3G11580" "AT5G55620" "AT4G11960" "AT4G22270"
## [877] "AT4G33960" "AT1G79360" "AT4G37070" "AT4G18360" "AT3G02520" "AT3G62260"
## [883] "AT4G24060" "AT5G51810" "AT4G05200" "AT5G53590" "AT3G25570" "AT2G38820"
## [889] "AT1G28190" "AT4G13840" "AT1G47890" "AT4G26520" "AT3G52340" "AT1G29070"
## [895] "AT3G03341" "AT5G37740" "AT2G40955" "AT1G56120" "AT1G54270" "AT2G17220"
## [901] "AT4G37180" "AT4G23160" "AT2G31940" "AT1G66880" "AT2G41090" "AT4G13260"
## [907] "AT5G42050" "AT5G61380" "AT5G15970" "AT2G23680" "ATCG00010" "AT1G64680"
## [913] "AT2G38340" "AT1G79520" "AT4G13345" "AT2G41850" "AT3G48740" "AT3G53540"
## [919] "AT3G16410" "AT2G15970" "AT4G24040" "AT3G18610" "AT5G09660" "AT2G44130"
## [925] "AT4G35690" "AT4G10430" "AT1G66970" "AT3G43720" "AT4G10955" "AT4G35720"
## [931] "AT5G14740" "AT3G16400" "AT4G24450" "AT1G36730" "AT3G11180" "AT5G04140"
## [937] "AT3G46780" "AT1G05780" "AT1G08230" "AT3G11840" "AT4G00955" "AT5G57560"
## [943] "AT4G27830" "AT4G22960" "AT1G77670" "AT5G50950" "AT5G48250" "AT1G14040"
## [949] "AT1G54290" "AT3G47510" "AT3G49940" "AT1G20630" "AT3G04030" "AT1G60610"
## [955] "ATCG00020" "AT3G48920" "AT2G47520" "AT1G55260" "AT5G54390" "AT1G62975"
## [961] "AT3G25620" "AT3G14620" "AT1G26730" "AT4G31270" "AT3G27210" "AT5G47650"
## [967] "AT2G21330" "AT4G26490" "AT5G53870" "AT1G69252" "AT4G24960" "AT2G44970"
## [973] "AT1G09415" "AT3G26740" "AT5G12890" "AT3G63140" "AT2G32100" "AT4G28750"
## [979] "AT2G34650" "AT1G07480" "AT5G03180" "AT4G34230" "AT3G01120" "AT5G47660"
## [985] "AT5G27750" "AT4G32295" "AT5G39080" "AT3G25910" "AT5G57240" "AT2G47240"
## [991] "AT1G01680" "AT2G02100" "AT4G37310" "AT5G17370" "AT1G05690" "AT1G16500"
## [997] "AT4G38470" "AT5G24210" "AT5G65730" "AT4G30630" "AT1G49840" "AT4G13180"
## [1003] "AT4G24340" "AT1G49450" "AT5G13360" "AT1G02450" "AT5G52300" "AT2G40020"
## [1009] "AT1G53560" "AT2G29470" "AT5G12270" "AT5G02030" "AT3G53235" "AT5G49450"
## [1015] "AT1G53670" "AT1G47510" "AT1G65500" "AT5G67245" "AT4G25100" "AT1G75280"
## [1021] "AT3G61080" "AT3G55290" "AT1G76100" "AT5G02790" "AT2G18193" "ATCG00800"
## [1027] "AT1G54310" "AT1G61440" "AT1G77220" "AT3G49160" "AT2G36307" "AT5G66780"
## [1033] "AT2G03975" "AT5G14700" "AT2G45760" "AT4G08780" "AT5G14590" "AT1G27300"
## [1039] "AT3G26220" "AT5G38030" "AT5G23220" "AT5G50160" "AT4G16760" "AT4G16670"
## [1045] "AT2G32560" "AT1G02670" "AT4G34135" "AT4G29270" "AT3G45300" "AT5G48180"
## [1051] "AT1G68540" "AT2G05440" "AT4G14930" "AT1G61480" "AT1G12780" "AT1G72190"
## [1057] "AT4G19870" "AT2G26250" "AT3G50820" "AT4G14746" "AT4G30450" "AT4G15765"
## [1063] "AT2G45770" "AT5G19875" "AT3G11900" "AT2G35920" "at1g66725" "AT3G08770"
## [1069] "AT1G18710" "AT1G53640" "AT3G48690" "AT5G18310" "AT3G59400" "AT3G27027"
## [1075] "AT5G24150" "AT3G44880" "AT3G04720" "AT1G12820" "AT2G37220" "AT4G15530"
## [1081] "AT5G19880" "AT2G30570" "AT1G70800" "AT2G46270" "AT3G13310" "AT3G03670"
## [1087] "AT1G80590" "AT2G13360" "AT5G16040" "AT3G16910" "AT5G13550" "AT5G14410"
## [1093] "AT3G20810" "AT1G51805" "AT3G06490" "AT4G15630" "AT5G54130" "AT3G02150"
## [1099] "AT1G66830" "AT4G05180" "AT1G33110" "AT5G64220" "AT2G39850" "AT1G12860"
## [1105] "AT3G52870" "AT1G47610" "AT1G74710" "AT3G03890" "AT4G38970" "AT1G08125"
## [1111] "AT5G66670" "AT1G28660" "AT1G56650" "AT5G33210" "AT3G14780" "AT1G52230"
## [1117] "AT2G24430" "AT3G01470" "AT5G26000" "AT3G14560" "AT2G21140" "AT2G26150"
## [1123] "AT3G09360" "AT1G31580" "AT5G51990" "AT2G18735" "AT3G20820" "AT2G34860"
## [1129] "AT1G61660" "AT3G27880" "AT3G20475" "AT2G05070" "AT1G45249" "AT1G04310"
## [1135] "AT4G22260" "AT2G41660" "AT2G20570" "AT1G71200" "ATCG00780" "AT2G18890"
## [1141] "AT1G12900" "AT5G06090" "AT5G23680" "AT5G47060" "AT2G34600" "AT5G28030"
## [1147] "AT1G08380" "AT5G25630" "AT3G45160" "AT1G63370" "AT5G62520" "AT2G27389"
## [1153] "AT2G26550" "AT4G16990" "AT3G26180" "AT3G17611" "AT3G62130" "AT5G27920"
## [1159] "AT5G58640" "AT5G01550" "AT2G18500" "AT3G03170" "AT3G09795" "AT1G18485"
## [1165] "AT5G64430" "AT2G02061" "AT3G55800" "AT3G12230" "ATCG00790" "ATCG00950"
## [1171] "ATCG01180" "AT1G42970" "AT2G07180" "AT2G40900" "AT3G12502" "AT2G21150"
## [1177] "AT1G18730" "AT2G21180" "AT4G28140" "AT1G66980" "AT1G28470" "AT3G63190"
## [1183] "AT5G54300" "AT5G18270" "AT2G14610" "AT4G13495" "AT1G20693" "AT4G00750"
## [1189] "AT1G54040" "AT1G19200" "AT3G08760" "AT1G02750" "AT5G17860" "ATCG00470"
## [1195] "AT3G62100" "AT5G59030" "ATCG00830" "ATCG01310" "AT3G58550" "AT2G36080"
## [1201] "AT4G10960" "AT3G59200" "AT1G04800" "AT1G09910" "AT3G51730" "ATCG00760"
## [1207] "AT3G03535" "AT1G65660" "AT5G12900" "AT5G44400" "AT1G63360" "AT2G38230"
## [1213] "AT4G12940" "AT3G47960" "AT2G28400" "AT5G47000" "AT5G39330" "AT1G68010"
## [1219] "AT2G48120" "AT1G32060" "AT3G46530" "AT3G10040" "AT2G25460" "AT1G30380"
## [1225] "AT5G10760" "AT2G48100" "AT4G29930" "AT1G67090" "AT2G18720" "AT1G15640"
## [1231] "AT4G16900" "AT5G67370" "AT3G48310" "AT2G32230" "AT5G54270" "AT4G19730"
## [1237] "AT1G06645" "AT2G26500" "AT1G66173" "AT1G30610" "AT5G13210" "AT1G52220"
## [1243] "AT2G04570" "AT3G14490" "AT4G06985" "AT1G64710" "AT4G12330" "AT5G15780"
## [1249] "AT4G00270" "AT1G52720"DEG summary
Here is a heatmap of all the differentially expressed genes.
degs <- unique(c(del3_up, del3_dn,
del5_up, del5_dn,
der3_up, der3_dn,
der5_up, der5_dn))
xxx <- xx/colSums(xx)*1e6
deg_mx <- as.matrix(xxx[which(rownames(xxx) %in% degs),])
colfunc <- colorRampPalette(c("blue", "white", "red"))
heatmap.2(deg_mx,col=colfunc(25),cexCol=0.8,trace="none",scale="row",margin=c(10,10),main="all samples")
degs_leaf <- unique(c(del3_up, del3_dn, del5_up, del5_dn))
leafx <- leaf/colSums(leaf)*1e6
deg_mx <- as.matrix(leaf[which(rownames(leaf) %in% degs_leaf),])
colfunc <- colorRampPalette(c("blue", "white", "red"))
heatmap.2(deg_mx,col=colfunc(25),cexCol=0.8,trace="none",scale="row",margin=c(10,10),main="leaf samples")
degs_root <- unique(c(der3_up, der3_dn, der5_up, der5_dn))
rootx <- root/colSums(root)*1e6
deg_mx <- as.matrix(root[which(rownames(root) %in% degs_root),])
colfunc <- colorRampPalette(c("blue", "white", "red"))
heatmap.2(deg_mx,col=colfunc(25),cexCol=0.8,trace="none",scale="row",margin=c(10,10),main="root samples")
Pathway analysis
Mapman pathways last modified in 2012 and used in the previous RNA-seq analysis. First I’ll strt with unidimensional analysis.
genesets <- gmt_import("../baseline/ref/Ath_AGI_LOCUS_TAIR10_Aug2012.txt.gmt")
gt <- read.table("../baseline/ref/Arabidopsis_thaliana.TAIR10.46.geneaccession2symbol.tsv",
fill=TRUE)
m <- mitch_import(x=as.data.frame(del3), DEtype="deseq2",geneTable=gt)## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21662## Note: no. genes in output = 21359## Note: estimated proportion of input genes in output = 0.986del3m <- mitch_calc(x=m,genesets=genesets,priority="effect",minsetsize=5)## Note: Enrichments with large effect sizes may not be
## statistically significant.mitch_barplot(del3m)
unlink("del3m_mitch.html")
capture.output(
mitch_report(del3m, outfile="del3m_mitch.html"),
file = "/dev/null", append = FALSE,
type = c("output", "message"), split = FALSE)## Dataset saved as " /tmp/RtmphbqrlE/del3m_mitch.rds ".##
##
## processing file: mitch.Rmd## Contour plot does not apply to unidimensional analysis.## output file: /mnt/bfx4/tohidul/seasol_2021-03/mitch.knit.md##
## Output created: /tmp/RtmphbqrlE/mitch_report.html
m <- mitch_import(x=as.data.frame(del5),DEtype="deseq2",geneTable=gt)## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21610## Note: no. genes in output = 21307## Note: estimated proportion of input genes in output = 0.986del5m <- mitch_calc(x=m,genesets=genesets,priority="effect",minsetsize=5)## Note: Enrichments with large effect sizes may not be
## statistically significant.mitch_barplot(del5m)
unlink("del5m_mitch.html")
capture.output(
mitch_report(del5m, outfile="del5m_mitch.html"),
file = "/dev/null", append = FALSE,
type = c("output", "message"), split = FALSE)## Dataset saved as " /tmp/RtmphbqrlE/del5m_mitch.rds ".##
##
## processing file: mitch.Rmd## Contour plot does not apply to unidimensional analysis.## output file: /mnt/bfx4/tohidul/seasol_2021-03/mitch.knit.md##
## Output created: /tmp/RtmphbqrlE/mitch_report.html
m <- mitch_import(x=as.data.frame(der3),DEtype="deseq2",geneTable=gt)## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21774## Note: no. genes in output = 21486## Note: estimated proportion of input genes in output = 0.987der3m <- mitch_calc(x=m,genesets=genesets,priority="effect",minsetsize=5)## Note: Enrichments with large effect sizes may not be
## statistically significant.mitch_barplot(der3m)
unlink("der3m_mitch.html")
capture.output(
mitch_report(der3m, outfile="der3m_mitch.html"),
file = "/dev/null", append = FALSE,
type = c("output", "message"), split = FALSE)## Dataset saved as " /tmp/RtmphbqrlE/der3m_mitch.rds ".##
##
## processing file: mitch.Rmd## Contour plot does not apply to unidimensional analysis.## output file: /mnt/bfx4/tohidul/seasol_2021-03/mitch.knit.md##
## Output created: /tmp/RtmphbqrlE/mitch_report.html
m <- mitch_import(x=as.data.frame(der5),DEtype="deseq2",geneTable=gt)## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21503## Note: no. genes in output = 21222## Note: estimated proportion of input genes in output = 0.987der5m <- mitch_calc(x=m,genesets=genesets,priority="effect",minsetsize=5)## Note: Enrichments with large effect sizes may not be
## statistically significant.mitch_barplot(der5m)
unlink("der5m_mitch.html")
capture.output(
mitch_report(der5m, outfile="der5m_mitch.html"),
file = "/dev/null", append = FALSE,
type = c("output", "message"), split = FALSE)## Dataset saved as " /tmp/RtmphbqrlE/der5m_mitch.rds ".##
##
## processing file: mitch.Rmd## Contour plot does not apply to unidimensional analysis.## output file: /mnt/bfx4/tohidul/seasol_2021-03/mitch.knit.md##
## Output created: /tmp/RtmphbqrlE/mitch_report.html
Next, multidimensional analysis.
l <- list("del3"=del3,"del5"=del5,
"der3"=der3, "der5"=der5)
m <- mitch_import(x=l,DEtype="deseq2",geneTable=gt)## Note: Mean no. genes in input = 21637.25## Note: no. genes in output = 19846## Note: estimated proportion of input genes in output = 0.917# effect size
res <- mitch_calc(x=m,genesets=genesets,priority="effect",minsetsize=5)## Note: Enrichments with large effect sizes may not be
## statistically significant.top <- subset(res$enrichment_result,p.adjustMANOVA<0.05)
kbl(head(top,30)) %>% kable_paper("hover", full_width = F)| set | setSize | pMANOVA | s.del3 | s.del5 | s.der3 | s.der5 | p.del3 | p.del5 | p.der3 | p.der5 | s.dist | SD | p.adjustMANOVA | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 374 | SIGNALLING_RECEPTOR_KINASES_LEUCINE_RICH_REPEAT_V | 8 | 0.0001360 | 0.8209497 | 0.4635548 | 0.5835770 | 0.8026515 | 0.0000578 | 0.0231777 | 0.0042569 | 0.0000843 | 1.3688144 | 0.1736369 | 0.0009415 |
| 434 | TRANSPORT_SULPHATE | 12 | 0.0000016 | -0.5711489 | -0.6016100 | -0.7414541 | -0.7536805 | 0.0006122 | 0.0003075 | 0.0000087 | 0.0000061 | 1.3438505 | 0.0940216 | 0.0000195 |
| 382 | SIGNALLING_RECEPTOR_KINASES_LEUCINE_RICH_REPEAT_XIII | 6 | 0.0040745 | 0.7348622 | 0.7972782 | 0.3083333 | 0.5037802 | 0.0018241 | 0.0007187 | 0.1909087 | 0.0325961 | 1.2347223 | 0.2240962 | 0.0164488 |
| 12 | AMINO_ACID_METABOLISM_SYNTHESIS_BRANCHED_CHAIN_GROUP_COMMON_BRANCHED-CHAIN_AMINO_ACID_AMINOTRANSFERASE | 6 | 0.0038640 | 0.7287130 | 0.7479839 | 0.1982527 | 0.5758233 | 0.0019923 | 0.0015079 | 0.4003803 | 0.0145790 | 1.2088751 | 0.2548755 | 0.0158932 |
| 375 | SIGNALLING_RECEPTOR_KINASES_LEUCINE_RICH_REPEAT_VI | 10 | 0.0001532 | 0.4131377 | 0.4368219 | 0.6870236 | 0.7580863 | 0.0236800 | 0.0167572 | 0.0001682 | 0.0000330 | 1.1866729 | 0.1745054 | 0.0010438 |
| 27 | CELL_WALL_CELLULOSE_SYNTHESIS | 12 | 0.0000670 | 0.4317502 | 0.4749756 | 0.6191977 | 0.7138331 | 0.0096039 | 0.0043843 | 0.0002036 | 0.0000185 | 1.1423544 | 0.1301872 | 0.0005215 |
| 216 | PROTEIN_POSTRANSLATIONAL_MODIFICATION_KINASE_RECEPTOR_LIKE_CYTOPLASMATIC_KINASE_V | 8 | 0.0055658 | 0.5276742 | 0.3626248 | 0.5206926 | 0.7157224 | 0.0097492 | 0.0757178 | 0.0107600 | 0.0004550 | 1.0923900 | 0.1444392 | 0.0209198 |
| 250 | PS_CALVIN_CYCLE_RUBISCO_INTERACTING | 6 | 0.0001168 | 0.4398522 | 0.8118784 | -0.4585685 | 0.2823589 | 0.0620670 | 0.0005726 | 0.0517488 | 0.2310290 | 1.0689378 | 0.5333672 | 0.0008346 |
| 17 | BIODEGRADATION_OF_XENOBIOTICS_LACTOYLGLUTATHIONE_LYASE | 9 | 0.0000021 | -0.0705360 | 0.4644800 | -0.5766273 | -0.7587785 | 0.7140591 | 0.0158224 | 0.0027380 | 0.0000807 | 1.0625257 | 0.5499616 | 0.0000247 |
| 257 | PS_LIGHTREACTION_PHOTOSYSTEM_I_PSI_POLYPEPTIDE_SUBUNITS | 16 | 0.0000000 | 0.0570159 | 0.6461737 | -0.7976362 | 0.0221634 | 0.6929652 | 0.0000076 | 0.0000000 | 0.8780190 | 1.0283511 | 0.5933520 | 0.0000000 |
| 231 | PROTEIN_SYNTHESIS_RIBOSOMAL_RNA | 12 | 0.0000354 | -0.4494135 | 0.0733505 | -0.6013075 | -0.6698598 | 0.0070232 | 0.6599783 | 0.0003096 | 0.0000586 | 1.0087793 | 0.3363003 | 0.0003084 |
| 254 | PS_LIGHTREACTION_PHOTOSYSTEM_II_LHC-II | 14 | 0.0000000 | 0.0426223 | 0.5722137 | -0.8028511 | 0.1701075 | 0.7824639 | 0.0002093 | 0.0000002 | 0.2704699 | 1.0013749 | 0.5781209 | 0.0000000 |
| 428 | TRANSPORT_P-_AND_V-ATPASES_H+-TRANSPORTING_TWO-SECTOR_ATPASE | 7 | 0.0000002 | -0.1183311 | 0.3575137 | 0.5919293 | -0.6987607 | 0.5877265 | 0.1014224 | 0.0066846 | 0.0013659 | 0.9901844 | 0.5704051 | 0.0000028 |
| 335 | SECONDARY_METABOLISM_FLAVONOIDS_ANTHOCYANINS_ANTHOCYANIN_5-AROMATIC_ACYLTRANSFERASE | 7 | 0.0000619 | 0.3849920 | 0.5918573 | -0.4685792 | -0.5049578 | 0.0777485 | 0.0066912 | 0.0318004 | 0.0206892 | 0.9864394 | 0.5695203 | 0.0004962 |
| 408 | TCA_/_ORG_TRANSFORMATION_OTHER_ORGANIC_ACID_TRANSFORMATONS_CYT_MDH | 5 | 0.0181898 | -0.5965728 | 0.1204274 | -0.3365455 | -0.6863868 | 0.0208751 | 0.6409818 | 0.1925007 | 0.0078583 | 0.9771343 | 0.3619314 | 0.0495673 |
| 39 | CELL_WALL_PRECURSOR_SYNTHESIS_GAE | 6 | 0.0073634 | 0.4958333 | 0.4894153 | 0.6726310 | 0.0876344 | 0.0354387 | 0.0378864 | 0.0043252 | 0.7100996 | 0.9723633 | 0.2475113 | 0.0258369 |
| 276 | RNA_REGULATION_OF_TRANSCRIPTION_ARF,_AUXIN_RESPONSE_FACTOR_FAMILY | 15 | 0.0000626 | 0.4850083 | 0.1144101 | 0.5205823 | 0.6443077 | 0.0011438 | 0.4429902 | 0.0004809 | 0.0000155 | 0.9666753 | 0.2282287 | 0.0004962 |
| 255 | PS_LIGHTREACTION_PHOTOSYSTEM_II_PSII_POLYPEPTIDE_SUBUNITS | 32 | 0.0000000 | 0.0547340 | 0.6405351 | -0.6450143 | -0.2563686 | 0.5920848 | 0.0000000 | 0.0000000 | 0.0120764 | 0.9460704 | 0.5429636 | 0.0000000 |
| 3 | AMINO_ACID_METABOLISM_DEGRADATION_BRANCHED_CHAIN_GROUP_SHARED | 7 | 0.0152655 | -0.2912085 | -0.3815356 | -0.7335263 | -0.3429536 | 0.1821398 | 0.0804528 | 0.0007763 | 0.1161168 | 0.9413022 | 0.2009176 | 0.0446255 |
| 55 | DNA_SYNTHESIS/CHROMATIN_STRUCTURE_HISTONE_CORE_H4 | 8 | 0.0012936 | -0.5091491 | 0.1845952 | -0.3884716 | -0.6554466 | 0.0126367 | 0.3659433 | 0.0570800 | 0.0013246 | 0.9347880 | 0.3677180 | 0.0064830 |
| 252 | PS_LIGHTREACTION_NADH_DH | 9 | 0.0000249 | -0.1632695 | 0.5261380 | -0.6351487 | -0.3897263 | 0.3963626 | 0.0062692 | 0.0009674 | 0.0429090 | 0.9267031 | 0.4997384 | 0.0002411 |
| 186 | OPP_OXIDATIVE_PP_6-PHOSPHOGLUCONATE_DEHYDROGENASE | 7 | 0.0000364 | -0.3849056 | 0.5990293 | 0.4654684 | -0.2036033 | 0.0778152 | 0.0060566 | 0.0329530 | 0.3509158 | 0.8747020 | 0.4859569 | 0.0003108 |
| 87 | LIPID_METABOLISM_FA_DESATURATION_DESATURASE | 5 | 0.0148524 | 0.5489743 | 0.6067134 | -0.1928633 | -0.2101809 | 0.0335126 | 0.0187981 | 0.4551720 | 0.4157136 | 0.8665138 | 0.4506396 | 0.0437545 |
| 30 | CELL_WALL_CELL_WALL_PROTEINS_AGPS_AGP | 38 | 0.0000000 | 0.4810311 | 0.3839039 | 0.4609435 | 0.3815391 | 0.0000003 | 0.0000421 | 0.0000009 | 0.0000469 | 0.8583787 | 0.0516249 | 0.0000004 |
| 94 | LIPID_METABOLISM_LIPID_DEGRADATION_BETA-OXIDATION_ACYL_COA_DH | 6 | 0.0027297 | 0.2897849 | 0.1646001 | -0.4205645 | -0.6535786 | 0.2189918 | 0.4850559 | 0.0744247 | 0.0055615 | 0.8456406 | 0.4542698 | 0.0121445 |
| 153 | MITOCHONDRIAL_ELECTRON_TRANSPORT_/_ATP_SYNTHESIS_NADH-DH_COMPLEX_I | 6 | 0.0124383 | -0.4630376 | 0.2833501 | -0.2951109 | -0.5665323 | 0.0495096 | 0.2293956 | 0.2106405 | 0.0162499 | 0.8382961 | 0.3793187 | 0.0390151 |
| 411 | TCA_/_ORG_TRANSFORMATION_TCA_SUCCINATE_DEHYDROGENASE | 5 | 0.0128271 | -0.1488332 | 0.5725820 | -0.3555365 | -0.4732725 | 0.5643975 | 0.0266013 | 0.1685866 | 0.0668460 | 0.8368958 | 0.4688198 | 0.0396638 |
| 240 | PROTEIN_SYNTHESIS_RIBOSOME_BIOGENESIS_PRE-RRNA_PROCESSING_AND_MODIFICATIONS_WD-REPEAT_PROTEINS | 6 | 0.0000315 | -0.3816868 | 0.2497648 | -0.2012097 | 0.6703293 | 0.1054329 | 0.2893948 | 0.3933902 | 0.0044600 | 0.8354005 | 0.4723941 | 0.0002857 |
| 403 | STRESS_BIOTIC_RESPIRATORY_BURST | 8 | 0.0012195 | -0.1723838 | -0.2324201 | 0.5326772 | 0.5698533 | 0.3985080 | 0.2549791 | 0.0090779 | 0.0052507 | 0.8319934 | 0.4360839 | 0.0061824 |
| 376 | SIGNALLING_RECEPTOR_KINASES_LEUCINE_RICH_REPEAT_VII | 9 | 0.0026247 | 0.0520072 | 0.4578705 | 0.3259285 | 0.6099993 | 0.7870377 | 0.0173764 | 0.0904279 | 0.0015290 | 0.8310708 | 0.2367068 | 0.0117976 |
rownames(top) <- top[,1]
top <- top[1:50,4:7]
colfunc <- colorRampPalette(c("blue", "white", "red"))
colnames(top) <- gsub("s\\.","",colnames(top))
heatmap.2( as.matrix(top), col=colfunc(25),
scale="none",Colv=FALSE,trace="none", dendrogram="row",
margins = c(5,25), cexCol=0.8 , cexRow=0.7, main="Top genes sets by effect size (FDR<0.05)")
unlink("mapman_report_eff.html")
capture.output(
mitch_report(res,outfile=paste("mapman_report_eff.html"))
, file = "/dev/null", append = FALSE,
type = c("output", "message"), split = FALSE)## Dataset saved as " /tmp/RtmphbqrlE/mapman_report_eff.rds ".##
##
## processing file: mitch.Rmd##
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output file: /mnt/bfx4/tohidul/seasol_2021-03/mitch.knit.md
##
##
## Output created: /tmp/RtmphbqrlE/mitch_report.html
Focus on ROS
DEL3 contrast
customsets <- c("MISC_GLUTATHIONE_S_TRANSFERASES",
"MISC_PEROXIDASES",
"REDOX_DISMUTASES_AND_CATALASES",
"REDOX_GLUTAREDOXINS")
customsets <- genesets[which(names(genesets) %in% customsets)]
m <- mitch_import(x=as.data.frame(del3), DEtype="deseq2",geneTable=gt)## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21662## Note: no. genes in output = 21359## Note: estimated proportion of input genes in output = 0.986del3m <- mitch_calc(x=m,genesets=customsets,priority="effect",minsetsize=5)## Note: Enrichments with large effect sizes may not be
## statistically significant.del3m$enrichment_result %>%
kbl() %>%
kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 3 | REDOX_DISMUTASES_AND_CATALASES | 11 | 0.1280015 | 0.2650280 | 0.2189188 |
| 2 | MISC_PEROXIDASES | 61 | 0.0398773 | -0.1521300 | 0.1595093 |
| 4 | REDOX_GLUTAREDOXINS | 33 | 0.1641891 | -0.1399259 | 0.2189188 |
| 1 | MISC_GLUTATHIONE_S_TRANSFERASES | 51 | 0.9183278 | -0.0083003 | 0.9183278 |
mitch_barplot(del3m)
vioplot(del3m$detailed_sets,horizontal=TRUE,las=1) ; grid()
#unlink("del3m_redox.html")
#capture.output(
# mitch_report(del3m, outfile="del3m_redox.html"),
# file = "/dev/null", append = FALSE,
# type = c("output", "message"), split = FALSE)DEL5
m <- mitch_import(x=as.data.frame(del5), DEtype="deseq2",geneTable=gt)## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21610## Note: no. genes in output = 21307## Note: estimated proportion of input genes in output = 0.986del5m <- mitch_calc(x=m,genesets=customsets,priority="effect",minsetsize=5)## Note: Enrichments with large effect sizes may not be
## statistically significant.del5m$enrichment_result %>%
kbl() %>%
kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 3 | REDOX_DISMUTASES_AND_CATALASES | 11 | 0.0288507 | 0.3805495 | 0.1154029 |
| 1 | MISC_GLUTATHIONE_S_TRANSFERASES | 51 | 0.2373320 | 0.0956519 | 0.4746641 |
| 4 | REDOX_GLUTAREDOXINS | 38 | 0.8427585 | 0.0185964 | 0.9730566 |
| 2 | MISC_PEROXIDASES | 60 | 0.9730566 | -0.0025211 | 0.9730566 |
mitch_barplot(del5m)
vioplot(del5m$detailed_sets,horizontal=TRUE,las=1) ; grid()
#unlink("del5m_redox.html")
#capture.output(
# mitch_report(del5m, outfile="del5m_redox.html"),
# file = "/dev/null", append = FALSE,
# type = c("output", "message"), split = FALSE)DER3
m <- mitch_import(x=as.data.frame(der3), DEtype="deseq2",geneTable=gt)## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21774## Note: no. genes in output = 21486## Note: estimated proportion of input genes in output = 0.987der3m <- mitch_calc(x=m,genesets=customsets,priority="effect",minsetsize=5)## Note: Enrichments with large effect sizes may not be
## statistically significant.der3m$enrichment_result %>%
kbl() %>%
kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 2 | MISC_PEROXIDASES | 63 | 0.0013972 | 0.2327457 | 0.0055889 |
| 4 | REDOX_GLUTAREDOXINS | 29 | 0.0416614 | 0.2185269 | 0.0555485 |
| 1 | MISC_GLUTATHIONE_S_TRANSFERASES | 53 | 0.0130669 | -0.1970713 | 0.0261337 |
| 3 | REDOX_DISMUTASES_AND_CATALASES | 11 | 0.9100535 | 0.0196719 | 0.9100535 |
mitch_barplot(der3m)
vioplot(der3m$detailed_sets,horizontal=TRUE,las=1) ; grid()
unlink("der3m_redox.html")
capture.output(
mitch_report(der3m, outfile="der3m_redox.html"),
file = "/dev/null", append = FALSE,
type = c("output", "message"), split = FALSE)## Dataset saved as " /tmp/RtmphbqrlE/der3m_redox.rds ".##
##
## processing file: mitch.Rmd## Contour plot does not apply to unidimensional analysis.## output file: /mnt/bfx4/tohidul/seasol_2021-03/mitch.knit.md##
## Output created: /tmp/RtmphbqrlE/mitch_report.html
DER5
m <- mitch_import(x=as.data.frame(der5), DEtype="deseq2",geneTable=gt)## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 21503## Note: no. genes in output = 21222## Note: estimated proportion of input genes in output = 0.987der5m <- mitch_calc(x=m,genesets=customsets,priority="effect",minsetsize=5)## Note: Enrichments with large effect sizes may not be
## statistically significant.der5m$enrichment_result %>%
kbl() %>%
kable_paper("hover", full_width = F)| set | setSize | pANOVA | s.dist | p.adjustANOVA | |
|---|---|---|---|---|---|
| 1 | MISC_GLUTATHIONE_S_TRANSFERASES | 52 | 0.0000255 | -0.3374659 | 0.0001020 |
| 3 | REDOX_DISMUTASES_AND_CATALASES | 11 | 0.0731615 | -0.3120036 | 0.0984069 |
| 4 | REDOX_GLUTAREDOXINS | 30 | 0.0738052 | -0.1885900 | 0.0984069 |
| 2 | MISC_PEROXIDASES | 62 | 0.6370520 | 0.0346485 | 0.6370520 |
mitch_barplot(der5m)
vioplot(der5m$detailed_sets,horizontal=TRUE,las=1) ; grid()
unlink("der5m_redox.html")
capture.output(
mitch_report(der5m, outfile="der5m_redox.html"),
file = "/dev/null", append = FALSE,
type = c("output", "message"), split = FALSE)## Dataset saved as " /tmp/RtmphbqrlE/der5m_redox.rds ".##
##
## processing file: mitch.Rmd## Contour plot does not apply to unidimensional analysis.## output file: /mnt/bfx4/tohidul/seasol_2021-03/mitch.knit.md##
## Output created: /tmp/RtmphbqrlE/mitch_report.html
Multidimensional
l <- list("del3"=del3,"del5"=del5,
"der3"=der3, "der5"=der5)
m <- mitch_import(x=l,DEtype="deseq2",geneTable=gt)## Note: Mean no. genes in input = 21637.25## Note: no. genes in output = 19846## Note: estimated proportion of input genes in output = 0.917# effect size
res <- mitch_calc(x=m,genesets=customsets,priority="effect",minsetsize=5)## Note: Enrichments with large effect sizes may not be
## statistically significant.top <- res$enrichment_result
kbl(head(top,30)) %>% kable_paper("hover", full_width = F)| set | setSize | pMANOVA | s.del3 | s.del5 | s.der3 | s.der5 | p.del3 | p.del5 | p.der3 | p.der5 | s.dist | SD | p.adjustMANOVA | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 3 | REDOX_DISMUTASES_AND_CATALASES | 11 | 0.0067272 | 0.2672640 | 0.3832390 | 0.0284392 | -0.3083393 | 0.1248236 | 0.0277413 | 0.8702704 | 0.0766037 | 0.5605212 | 0.3054218 | 0.0067272 |
| 1 | MISC_GLUTATHIONE_S_TRANSFERASES | 49 | 0.0000056 | -0.0190928 | 0.0802131 | -0.1912359 | -0.3903818 | 0.8171694 | 0.3314080 | 0.0205714 | 0.0000023 | 0.4424565 | 0.2065901 | 0.0000223 |
| 4 | REDOX_GLUTAREDOXINS | 28 | 0.0048060 | -0.1493520 | 0.1001651 | 0.2125665 | -0.1688436 | 0.1713705 | 0.3589686 | 0.0515588 | 0.1220238 | 0.3256251 | 0.1879931 | 0.0064080 |
| 2 | MISC_PEROXIDASES | 55 | 0.0000957 | -0.1586901 | -0.0029959 | 0.2787135 | 0.0164914 | 0.0417942 | 0.9693475 | 0.0003495 | 0.8324743 | 0.3211615 | 0.1813724 | 0.0001914 |
rownames(top) <- top[,1]
top <- top[,4:7]
colfunc <- colorRampPalette(c("blue", "white", "red"))
colnames(top) <- gsub("s\\.","",colnames(top))
heatmap.2( as.matrix(top), col=colfunc(25),
scale="none",Colv=FALSE,trace="none", dendrogram="row",
margins = c(5,25), cexCol=0.8 , cexRow=0.7, main="Selected gene sets")
unlink("multi_redox.html")
capture.output(
mitch_report(res,outfile=paste("multi_redox.html"))
, file = "/dev/null", append = FALSE,
type = c("output", "message"), split = FALSE)## Dataset saved as " /tmp/RtmphbqrlE/multi_redox.rds ".##
##
## processing file: mitch.Rmd##
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output file: /mnt/bfx4/tohidul/seasol_2021-03/mitch.knit.md
##
##
## Output created: /tmp/RtmphbqrlE/mitch_report.html
Session information
So you know what version of R and packages was used.
sessionInfo()## R version 4.0.3 (2020-10-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.2 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] parallel stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] pkgload_1.2.0 GGally_2.1.1
## [3] ggplot2_3.3.3 beeswarm_0.3.1
## [5] gtools_3.8.2 tibble_3.1.0
## [7] dplyr_1.0.5 echarts4r_0.4.0
## [9] vioplot_0.3.5 zoo_1.8-9
## [11] sm_2.2-5.6 UpSetR_1.4.0
## [13] eulerr_6.1.0 kableExtra_1.3.4
## [15] mitch_1.2.2 DESeq2_1.30.0
## [17] SummarizedExperiment_1.20.0 Biobase_2.50.0
## [19] MatrixGenerics_1.2.0 matrixStats_0.58.0
## [21] GenomicRanges_1.42.0 GenomeInfoDb_1.26.0
## [23] IRanges_2.24.0 S4Vectors_0.28.0
## [25] BiocGenerics_0.36.0 gplots_3.1.1
## [27] reshape2_1.4.4
##
## loaded via a namespace (and not attached):
## [1] colorspace_2.0-0 ellipsis_0.3.1 rprojroot_2.0.2
## [4] XVector_0.30.0 rstudioapi_0.13 farver_2.1.0
## [7] bit64_4.0.5 AnnotationDbi_1.52.0 fansi_0.4.2
## [10] xml2_1.3.2 splines_4.0.3 cachem_1.0.4
## [13] geneplotter_1.68.0 knitr_1.31 polyclip_1.10-0
## [16] jsonlite_1.7.2 annotate_1.68.0 shiny_1.6.0
## [19] compiler_4.0.3 httr_1.4.2 assertthat_0.2.1
## [22] Matrix_1.3-2 fastmap_1.1.0 later_1.1.0.1
## [25] prettyunits_1.1.1 htmltools_0.5.1.1 tools_4.0.3
## [28] gtable_0.3.0 glue_1.4.2 GenomeInfoDbData_1.2.4
## [31] Rcpp_1.0.6 jquerylib_0.1.3 vctrs_0.3.6
## [34] svglite_2.0.0 polylabelr_0.2.0 xfun_0.22
## [37] stringr_1.4.0 testthat_3.0.2 rvest_1.0.0
## [40] mime_0.10 lifecycle_1.0.0 XML_3.99-0.6
## [43] zlibbioc_1.36.0 MASS_7.3-53.1 scales_1.1.1
## [46] hms_1.0.0 promises_1.2.0.1 RColorBrewer_1.1-2
## [49] yaml_2.2.1 memoise_2.0.0 gridExtra_2.3
## [52] sass_0.3.1 reshape_0.8.8 stringi_1.5.3
## [55] RSQLite_2.2.4 highr_0.8 genefilter_1.72.0
## [58] desc_1.3.0 caTools_1.18.1 BiocParallel_1.24.1
## [61] rlang_0.4.10 pkgconfig_2.0.3 systemfonts_1.0.1
## [64] bitops_1.0-6 evaluate_0.14 lattice_0.20-41
## [67] purrr_0.3.4 labeling_0.4.2 htmlwidgets_1.5.3
## [70] bit_4.0.4 tidyselect_1.1.0 plyr_1.8.6
## [73] magrittr_2.0.1 R6_2.5.0 generics_0.1.0
## [76] DelayedArray_0.16.0 DBI_1.1.1 withr_2.4.1
## [79] pillar_1.5.1 survival_3.2-10 RCurl_1.98-1.3
## [82] crayon_1.4.1 KernSmooth_2.23-18 utf8_1.2.1
## [85] rmarkdown_2.7 progress_1.2.2 locfit_1.5-9.4
## [88] grid_4.0.3 blob_1.2.1 digest_0.6.27
## [91] webshot_0.5.2 xtable_1.8-4 httpuv_1.5.5
## [94] munsell_0.5.0 viridisLite_0.3.0 bslib_0.2.4
## [97] tcltk_4.0.3References
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