Effect of Mst1-TG in young and old mice
Mark Ziemann
2022-02-01
Source: https://github.com/markziemann/mst1tg_mito_rna-seq
Loading packages
# to be run in R4
suppressPackageStartupMessages({
library("tidyverse")
library("reshape2")
library("gplots")
library("mitch")
})Import profiling data
young <- read.csv("Mst1TG_young_deseq.tsv",sep="\t")
rownames(young) <- sapply((strsplit(rownames(young),"\\.")),"[[",1)
old <- read.csv("Mst1TG_old_deseq.tsv",sep="\t")
rownames(old) <- sapply((strsplit(rownames(old),"\\.")),"[[",1)
x <- list("young" = young , "old" = old)
# import these in again for heatmaps
young <- read.csv("Mst1TG_young_deseq.tsv",sep="\t")
old <- read.csv("Mst1TG_old_deseq.tsv",sep="\t")Gene sets
gsets <- gmt_import("../ref/ReactomePathways_mouse.gmt")
# gene accession to symbol mapping
gt <- read.csv("../ref/mart_export.txt",sep="\t")
gt <- gt[,c(1,4)]mitch
Lets begin with priority by significance.
yy <- mitch_import(x, DEtype="deseq2", geneTable=gt)## Note: Mean no. genes in input = 17755## Note: no. genes in output = 14877## Note: estimated proportion of input genes in output = 0.838res <- mitch_calc(yy, gsets, priority="significance")## Note: When prioritising by significance (ie: small
## p-values), large effect sizes might be missed.head(res$enrichment_result,20)## set
## 1175 The-citric-acid-(TCA)-cycle-and-respiratory-electron-transport
## 963 Respiratory-electron-transport,-ATP-synthesis-by-chemiosmotic-coupling,-and-heat-production-by-uncoupling-proteins.
## 962 Respiratory-electron-transport
## 601 Metabolism
## 635 Mitochondrial-translation
## 636 Mitochondrial-translation-elongation
## 638 Mitochondrial-translation-termination
## 637 Mitochondrial-translation-initiation
## 335 Extracellular-matrix-organization
## 193 Complex-I-biogenesis
## 1215 Translation
## 826 Protein-localization
## 633 Mitochondrial-protein-import
## 836 Pyruvate-metabolism-and-Citric-Acid-(TCA)-cycle
## 630 Mitochondrial-biogenesis
## 186 Collagen-biosynthesis-and-modifying-enzymes
## 208 Cristae-formation
## 629 Mitochondrial-Fatty-Acid-Beta-Oxidation
## 189 Collagen-formation
## 1023 Signal-Transduction
## setSize pMANOVA s.young s.old p.young p.old
## 1175 168 2.515849e-83 -0.8361385 -0.81430465 1.230669e-78 1.234084e-74
## 963 121 9.359276e-66 -0.8833095 -0.83745735 1.258076e-63 2.530445e-57
## 962 100 4.626085e-57 -0.9035826 -0.85861000 2.801421e-55 4.761159e-50
## 601 1615 2.726231e-49 -0.2001755 -0.22456349 9.652047e-40 1.236627e-49
## 635 94 6.954962e-44 -0.8253673 -0.75822286 1.108541e-43 4.243812e-37
## 636 88 2.901428e-41 -0.8273809 -0.75794817 3.378270e-41 8.105151e-35
## 638 88 4.505778e-41 -0.8254722 -0.75609175 5.147975e-41 1.179238e-34
## 637 88 1.348162e-40 -0.8214244 -0.74964501 1.253713e-40 4.304968e-34
## 335 228 1.350544e-38 0.4991275 0.45777569 1.410377e-38 1.080239e-32
## 193 54 1.621653e-33 -0.9302161 -0.90362325 2.281589e-32 1.245806e-30
## 1215 243 6.643594e-31 -0.4108691 -0.42384188 2.925991e-28 5.659389e-30
## 826 142 7.412507e-29 -0.5118837 -0.53720327 6.064025e-26 2.039938e-28
## 633 57 8.672171e-23 -0.7619007 -0.68645027 2.285529e-23 2.947540e-19
## 836 51 4.483657e-21 -0.7249612 -0.76031508 3.153090e-19 5.373685e-21
## 630 88 1.702298e-19 -0.5304265 -0.55687581 7.776007e-18 1.670651e-19
## 186 56 1.436322e-17 0.6369799 0.65537076 1.592143e-16 2.099903e-17
## 208 29 4.274261e-17 -0.9046104 -0.86083346 3.206166e-17 9.786321e-16
## 629 31 5.132212e-17 -0.8584391 -0.84985203 1.245379e-16 2.491625e-16
## 189 75 1.224413e-16 0.5455389 0.54164212 3.060851e-16 4.962533e-16
## 1023 1718 3.251919e-14 0.1166064 0.09353717 3.255389e-15 2.628458e-10
## s.dist SD p.adjustMANOVA
## 1175 1.1671417 0.015438895 3.288214e-80
## 963 1.2171978 0.032422401 6.116287e-63
## 962 1.2464641 0.031800425 2.015431e-54
## 601 0.3008305 0.017244941 8.907961e-47
## 635 1.1207734 0.047478264 1.818027e-41
## 636 1.1220716 0.049096367 6.320277e-39
## 638 1.1194102 0.049059420 8.412931e-39
## 637 1.1120727 0.050755696 2.202560e-38
## 335 0.6772643 0.029240169 1.961289e-36
## 193 1.2968565 0.018803954 2.119500e-31
## 1215 0.5903011 0.009173139 7.893798e-29
## 826 0.7420325 0.017903671 8.073456e-27
## 633 1.0255275 0.053351514 8.718867e-21
## 836 1.0505464 0.024998980 4.185814e-19
## 630 0.7690663 0.018702498 1.483269e-17
## 186 0.9139224 0.013004325 1.173296e-15
## 208 1.2487411 0.030954971 3.286152e-15
## 629 1.2079595 0.006071986 3.726556e-15
## 189 0.7687580 0.002755433 8.422672e-15
## 1023 0.1494866 0.016312415 2.125129e-12unlink("Mst1TG_young_and_old_sig_mitch.html")
# top N gene heatmap
mitch_report(res, outfile = "Mst1TG_young_and_old_sig_mitch.html")## Dataset saved as " /tmp/Rtmp0VANOs/Mst1TG_young_and_old_sig_mitch.rds ".##
##
## processing file: mitch.Rmd##
|
| | 0%
|
|.. | 3%
## inline R code fragments
##
##
|
|.... | 6%
## label: checklibraries (with options)
## List of 1
## $ echo: logi FALSE
##
##
|
|...... | 9%
## ordinary text without R code
##
##
|
|........ | 12%
## label: peek (with options)
## List of 1
## $ echo: logi FALSE
##
##
|
|.......... | 15%
## ordinary text without R code
##
##
|
|............ | 18%
## label: metrics (with options)
## List of 1
## $ echo: logi FALSE
##
##
|
|.............. | 21%
## ordinary text without R code
##
##
|
|................ | 24%
## label: scatterplot (with options)
## List of 5
## $ echo : logi FALSE
## $ fig.height: num 6
## $ fig.width : num 6.5
## $ message : logi FALSE
## $ warning : logi FALSE##
|
|................... | 26%
## ordinary text without R code
##
##
|
|..................... | 29%
## label: contourplot (with options)
## List of 5
## $ echo : logi FALSE
## $ fig.height: num 6
## $ fig.width : num 6.5
## $ warning : logi FALSE
## $ message : logi FALSE##
|
|....................... | 32%
## ordinary text without R code
##
##
|
|......................... | 35%
## label: input_geneset_metrics1 (with options)
## List of 2
## $ results: chr "asis"
## $ echo : logi FALSE
##
##
|
|........................... | 38%
## ordinary text without R code
##
##
|
|............................. | 41%
## label: input_geneset_metrics2 (with options)
## List of 5
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"##
|
|............................... | 44%
## ordinary text without R code
##
##
|
|................................. | 47%
## label: input_geneset_metrics3 (with options)
## List of 5
## $ results : chr "asis"
## $ echo : logi FALSE
## $ message : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7##
|
|................................... | 50%
## ordinary text without R code
##
##
|
|..................................... | 53%
## label: echart1d (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE
##
##
|
|....................................... | 56%
## label: echart2d (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE
##
##
|
|......................................... | 59%
## ordinary text without R code
##
##
|
|........................................... | 62%
## label: heatmap (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 10
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE##
|
|............................................. | 65%
## ordinary text without R code
##
##
|
|............................................... | 68%
## label: effectsize (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE
##
##
|
|................................................. | 71%
## ordinary text without R code
##
##
|
|................................................... | 74%
## label: results_table (with options)
## List of 2
## $ results: chr "asis"
## $ echo : logi FALSE
##
##
|
|...................................................... | 76%
## ordinary text without R code
##
##
|
|........................................................ | 79%
## label: results_table_complete (with options)
## List of 2
## $ results: chr "asis"
## $ echo : logi FALSE
##
##
|
|.......................................................... | 82%
## ordinary text without R code
##
##
|
|............................................................ | 85%
## label: detailed_geneset_reports1d (with options)
## List of 7
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 6
## $ fig.width : num 6
## $ out.width : chr "80%"
## $ comment : logi NA
## $ message : logi FALSE
##
##
|
|.............................................................. | 88%
## ordinary text without R code
##
##
|
|................................................................ | 91%
## label: detailed_geneset_reports2d (with options)
## List of 7
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 5
## $ fig.width : num 6
## $ out.width : chr "80%"
## $ comment : logi NA
## $ message : logi FALSE##
|
|.................................................................. | 94%
## ordinary text without R code
##
##
|
|.................................................................... | 97%
## label: session_info (with options)
## List of 3
## $ include: logi TRUE
## $ echo : logi TRUE
## $ results: chr "markup"
##
##
|
|......................................................................| 100%
## ordinary text without R code## output file: /mnt/bfx6/bfx/du_xiao/young_mst1tg/integrate/mitch.knit.md## /home/mdz/anaconda3/bin/pandoc +RTS -K512m -RTS /mnt/bfx6/bfx/du_xiao/young_mst1tg/integrate/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmp0VANOs/mitch_report.html --lua-filter /usr/lib/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/lib/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --standalone --section-divs --template /usr/lib/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header /tmp/Rtmp0VANOs/rmarkdown-str2293367beded.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'##
## Output created: /tmp/Rtmp0VANOs/mitch_report.html## [1] TRUE# heatmaps of top sets by significance
# colour scheme
colfunc <- colorRampPalette(c("blue", "white", "red"))
topsets <- head(res$enrichment_result,50)$set
mytopsets <- gsets[which(names( gsets ) %in% topsets)]
yo <- young[,7:ncol(young)]
colnames(yo) <- paste("y",colnames(yo))
ol <- old[,7:ncol(old)]
colnames(ol) <- paste("o",colnames(ol))
mx <- merge(yo,ol,by=0)
rownames(mx) <- mx$Row.names
mx$Row.names = NULL
i = 1
par(mar = c(10, 8, 8, 4) + 0.2)
for ( i in seq_along(mytopsets) ) {
g <- as.vector(unlist(mytopsets[i]))
symbol <- sapply((strsplit(rownames(mx)," ")),"[[",2)
z <- mx[which(symbol %in% g),]
SETNAME=names(mytopsets[i])
heatmap.2( as.matrix(z), col=colfunc(25),scale="row",
trace="none",margins = c(6,20), cexRow=.4, cexCol=.8)
mtext(SETNAME)
}
Now prioritise by effect size.
res <- mitch_calc(yy, gsets, priority = "effect")## Note: Enrichments with large effect sizes may not be
## statistically significant.head(res$enrichment_result,20)## set
## 361 Formation-of-ATP-by-chemiosmotic-coupling
## 193 Complex-I-biogenesis
## 176 Citric-acid-cycle-(TCA-cycle)
## 208 Cristae-formation
## 962 Respiratory-electron-transport
## 963 Respiratory-electron-transport,-ATP-synthesis-by-chemiosmotic-coupling,-and-heat-production-by-uncoupling-proteins.
## 629 Mitochondrial-Fatty-Acid-Beta-Oxidation
## 110 Branched-chain-amino-acid-catabolism
## 1175 The-citric-acid-(TCA)-cycle-and-respiratory-electron-transport
## 1298 rRNA-processing-in-the-mitochondrion
## 1304 tRNA-processing-in-the-mitochondrion
## 636 Mitochondrial-translation-elongation
## 635 Mitochondrial-translation
## 638 Mitochondrial-translation-termination
## 637 Mitochondrial-translation-initiation
## 632 Mitochondrial-iron-sulfur-cluster-biogenesis
## 440 Glyoxylate-metabolism-and-glycine-degradation
## 836 Pyruvate-metabolism-and-Citric-Acid-(TCA)-cycle
## 187 Collagen-chain-trimerization
## 633 Mitochondrial-protein-import
## setSize pMANOVA s.young s.old p.young p.old
## 361 16 1.292423e-10 -0.9329789 -0.9194031 1.017112e-10 1.887907e-10
## 193 54 1.621653e-33 -0.9302161 -0.9036232 2.281589e-32 1.245806e-30
## 176 22 2.511926e-13 -0.8942872 -0.8892751 3.711622e-13 5.015120e-13
## 208 29 4.274261e-17 -0.9046104 -0.8608335 3.206166e-17 9.786321e-16
## 962 100 4.626085e-57 -0.9035826 -0.8586100 2.801421e-55 4.761159e-50
## 963 121 9.359276e-66 -0.8833095 -0.8374574 1.258076e-63 2.530445e-57
## 629 31 5.132212e-17 -0.8584391 -0.8498520 1.245379e-16 2.491625e-16
## 110 21 2.430098e-11 -0.8328525 -0.8426674 3.838241e-11 2.259224e-11
## 1175 168 2.515849e-83 -0.8361385 -0.8143047 1.230669e-78 1.234084e-74
## 1298 22 1.564605e-11 -0.7831156 -0.8542333 2.002556e-10 3.928719e-12
## 1304 18 3.426684e-09 -0.7504019 -0.8415326 3.521252e-08 6.262141e-10
## 636 88 2.901428e-41 -0.8273809 -0.7579482 3.378270e-41 8.105151e-35
## 635 94 6.954962e-44 -0.8253673 -0.7582229 1.108541e-43 4.243812e-37
## 638 88 4.505778e-41 -0.8254722 -0.7560918 5.147975e-41 1.179238e-34
## 637 88 1.348162e-40 -0.8214244 -0.7496450 1.253713e-40 4.304968e-34
## 632 10 6.993237e-05 -0.7409968 -0.7750185 4.948957e-05 2.191278e-05
## 440 25 7.782677e-11 -0.7513547 -0.7477350 7.741915e-11 9.534951e-11
## 836 51 4.483657e-21 -0.7249612 -0.7603151 3.153090e-19 5.373685e-21
## 187 33 1.118654e-13 0.7367001 0.7402562 2.337306e-13 1.793245e-13
## 633 57 8.672171e-23 -0.7619007 -0.6864503 2.285529e-23 2.947540e-19
## s.dist SD p.adjustMANOVA
## 361 1.309867 0.009599542 4.826277e-09
## 193 1.296857 0.018803954 2.119500e-31
## 176 1.261174 0.003544080 1.492313e-11
## 208 1.248741 0.030954971 3.286152e-15
## 962 1.246464 0.031800425 2.015431e-54
## 963 1.217198 0.032422401 6.116287e-63
## 629 1.207960 0.006071986 3.726556e-15
## 110 1.184792 0.006940152 1.134335e-09
## 1175 1.167142 0.015438895 3.288214e-80
## 1298 1.158872 0.050287861 7.573845e-10
## 1304 1.127511 0.064439138 1.210453e-07
## 636 1.122072 0.049096367 6.320277e-39
## 635 1.120773 0.047478264 1.818027e-41
## 638 1.119410 0.049059420 8.412931e-39
## 637 1.112073 0.050755696 2.202560e-38
## 632 1.072255 0.024056946 9.451158e-04
## 440 1.060020 0.002559525 3.184758e-09
## 836 1.050546 0.024998980 4.185814e-19
## 187 1.044369 0.002514596 6.962290e-12
## 633 1.025527 0.053351514 8.718867e-21unlink("Mst1TG_young_and_old_eff_mitch.html")
mitch_report(res, outfile = "Mst1TG_young_and_old_eff_mitch.html")## Dataset saved as " /tmp/Rtmp0VANOs/Mst1TG_young_and_old_eff_mitch.rds ".##
##
## processing file: mitch.Rmd##
|
| | 0%
|
|.. | 3%
## inline R code fragments
##
##
|
|.... | 6%
## label: checklibraries (with options)
## List of 1
## $ echo: logi FALSE
##
##
|
|...... | 9%
## ordinary text without R code
##
##
|
|........ | 12%
## label: peek (with options)
## List of 1
## $ echo: logi FALSE
##
##
|
|.......... | 15%
## ordinary text without R code
##
##
|
|............ | 18%
## label: metrics (with options)
## List of 1
## $ echo: logi FALSE
##
##
|
|.............. | 21%
## ordinary text without R code
##
##
|
|................ | 24%
## label: scatterplot (with options)
## List of 5
## $ echo : logi FALSE
## $ fig.height: num 6
## $ fig.width : num 6.5
## $ message : logi FALSE
## $ warning : logi FALSE##
|
|................... | 26%
## ordinary text without R code
##
##
|
|..................... | 29%
## label: contourplot (with options)
## List of 5
## $ echo : logi FALSE
## $ fig.height: num 6
## $ fig.width : num 6.5
## $ warning : logi FALSE
## $ message : logi FALSE##
|
|....................... | 32%
## ordinary text without R code
##
##
|
|......................... | 35%
## label: input_geneset_metrics1 (with options)
## List of 2
## $ results: chr "asis"
## $ echo : logi FALSE
##
##
|
|........................... | 38%
## ordinary text without R code
##
##
|
|............................. | 41%
## label: input_geneset_metrics2 (with options)
## List of 5
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"##
|
|............................... | 44%
## ordinary text without R code
##
##
|
|................................. | 47%
## label: input_geneset_metrics3 (with options)
## List of 5
## $ results : chr "asis"
## $ echo : logi FALSE
## $ message : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7##
|
|................................... | 50%
## ordinary text without R code
##
##
|
|..................................... | 53%
## label: echart1d (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE
##
##
|
|....................................... | 56%
## label: echart2d (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE
##
##
|
|......................................... | 59%
## ordinary text without R code
##
##
|
|........................................... | 62%
## label: heatmap (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 10
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE##
|
|............................................. | 65%
## ordinary text without R code
##
##
|
|............................................... | 68%
## label: effectsize (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE
##
##
|
|................................................. | 71%
## ordinary text without R code
##
##
|
|................................................... | 74%
## label: results_table (with options)
## List of 2
## $ results: chr "asis"
## $ echo : logi FALSE
##
##
|
|...................................................... | 76%
## ordinary text without R code
##
##
|
|........................................................ | 79%
## label: results_table_complete (with options)
## List of 2
## $ results: chr "asis"
## $ echo : logi FALSE
##
##
|
|.......................................................... | 82%
## ordinary text without R code
##
##
|
|............................................................ | 85%
## label: detailed_geneset_reports1d (with options)
## List of 7
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 6
## $ fig.width : num 6
## $ out.width : chr "80%"
## $ comment : logi NA
## $ message : logi FALSE
##
##
|
|.............................................................. | 88%
## ordinary text without R code
##
##
|
|................................................................ | 91%
## label: detailed_geneset_reports2d (with options)
## List of 7
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 5
## $ fig.width : num 6
## $ out.width : chr "80%"
## $ comment : logi NA
## $ message : logi FALSE##
|
|.................................................................. | 94%
## ordinary text without R code
##
##
|
|.................................................................... | 97%
## label: session_info (with options)
## List of 3
## $ include: logi TRUE
## $ echo : logi TRUE
## $ results: chr "markup"
##
##
|
|......................................................................| 100%
## ordinary text without R code## output file: /mnt/bfx6/bfx/du_xiao/young_mst1tg/integrate/mitch.knit.md## /home/mdz/anaconda3/bin/pandoc +RTS -K512m -RTS /mnt/bfx6/bfx/du_xiao/young_mst1tg/integrate/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmp0VANOs/mitch_report.html --lua-filter /usr/lib/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/lib/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --standalone --section-divs --template /usr/lib/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header /tmp/Rtmp0VANOs/rmarkdown-str2293403f58c.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'##
## Output created: /tmp/Rtmp0VANOs/mitch_report.html## [1] TRUE# heatmaps of top sets by effect size
topsets <- head(res$enrichment_result,50)$set
mytopsets <- gsets[which(names( gsets ) %in% topsets)]
i=1
par(mar = c(10, 8, 8, 4) + 0.2)
for ( i in seq_along(mytopsets) ) {
g <- as.vector(unlist(mytopsets[i]))
symbol <- sapply((strsplit(rownames(mx)," ")),"[[",2)
z <- mx[which(symbol %in% g),]
SETNAME = names(mytopsets[i])
heatmap.2( as.matrix(z), col = colfunc(25),scale = "row",
trace="none",margins = c(6,20), cexRow = .4, cexCol = .8)
mtext(SETNAME)
}
Now prioritise by discordant effect size.
res <- mitch_calc(yy, gsets, priority = "SD")## Note: Prioritisation by SD after selecting sets with
## p.adjustMANOVA<=0.05.head(res$enrichment_result,20)## set
## 1171 Termination-of-O-glycan-biosynthesis
## 1111 Synaptic-adhesion-like-molecules
## 519 Interferon-alpha/beta-signaling
## 1174 The-canonical-retinoid-cycle-in-rods-(twilight-vision)
## 658 N-glycan-antennae-elongation-in-the-medial/trans-Golgi
## 166 Chemokine-receptors-bind-chemokines
## 730 O-linked-glycosylation-of-mucins
## 460 HS-GAG-biosynthesis
## 1266 WNT5A-dependent-internalization-of-FZD2,-FZD5-and-ROR2
## 461 HS-GAG-degradation
## 350 FOXO-mediated-transcription-of-oxidative-stress,-metabolic-and-neuronal-genes
## 1022 Sialic-acid-metabolism
## 285 Downregulation-of-SMAD2/3:SMAD4-transcriptional-activity
## 1126 Synthesis-of-active-ubiquitin:-roles-of-E1-and-E2-enzymes
## 1236 Triglyceride-catabolism
## 1242 Ubiquitin-Mediated-Degradation-of-Phosphorylated-Cdc25A
## 1290 p53-Independent-DNA-Damage-Response
## 1291 p53-Independent-G1/S-DNA-damage-checkpoint
## 86 Assembly-of-the-pre-replicative-complex
## 948 Regulation-of-ornithine-decarboxylase-(ODC)
## setSize pMANOVA s.young s.old p.young p.old
## 1171 10 1.115890e-03 0.39081187 -0.0052599717 0.0323685019 9.770257e-01
## 1111 15 1.732267e-03 0.28323689 -0.0347373615 0.0575633910 8.158480e-01
## 519 40 1.387142e-08 0.04785671 0.3600053919 0.6006283244 8.180409e-05
## 1174 12 4.087033e-04 0.24527413 0.5572149344 0.1412962416 8.309092e-04
## 658 20 2.410343e-04 0.35078414 0.0531197415 0.0066187051 6.809598e-01
## 166 20 2.501491e-03 0.29927980 0.0474321868 0.0205218841 7.135212e-01
## 730 32 1.254537e-05 0.38636746 0.1405776356 0.0001554919 1.688774e-01
## 460 23 1.159881e-04 0.43421476 0.1915455360 0.0003126898 1.118798e-01
## 1266 13 5.292945e-03 0.44633394 0.2064461373 0.0053319120 1.975302e-01
## 461 18 4.696817e-04 0.47066125 0.2343660034 0.0005463251 8.522719e-02
## 350 23 9.528103e-03 0.09551519 -0.1308914009 0.4279310937 2.773219e-01
## 1022 26 3.270409e-03 0.23833671 0.0168131646 0.0354594522 8.820684e-01
## 285 23 6.014951e-03 0.24809011 0.0279532376 0.0394778318 8.165394e-01
## 1126 29 3.254697e-03 -0.01472856 -0.2248485806 0.8908463045 3.615487e-02
## 1236 15 9.291510e-06 -0.50318037 -0.7077827121 0.0007405841 2.065018e-06
## 1242 48 2.720323e-05 -0.31450480 -0.1268151370 0.0001642006 1.286981e-01
## 1290 48 2.720323e-05 -0.31450480 -0.1268151370 0.0001642006 1.286981e-01
## 1291 48 2.720323e-05 -0.31450480 -0.1268151370 0.0001642006 1.286981e-01
## 86 64 6.669333e-05 -0.18632493 -0.0003354317 0.0099862346 9.962998e-01
## 948 46 3.967504e-05 -0.32015490 -0.1351077209 0.0001728409 1.130494e-01
## s.dist SD p.adjustMANOVA
## 1171 0.3908473 0.2800651 8.733342e-03
## 1111 0.2853591 0.2248417 1.271951e-02
## 519 0.3631723 0.2207225 4.316653e-07
## 1174 0.6088086 0.2205755 3.842987e-03
## 658 0.3547833 0.2104805 2.540579e-03
## 166 0.3030152 0.1780832 1.646570e-02
## 730 0.4111470 0.1737997 2.309409e-04
## 460 0.4745863 0.1715931 1.430155e-03
## 1266 0.4917662 0.1696263 3.158849e-02
## 461 0.5257846 0.1670860 4.292825e-03
## 350 0.1620361 0.1600936 4.845615e-02
## 1022 0.2389290 0.1566408 2.045179e-02
## 285 0.2496599 0.1556603 3.448045e-02
## 1126 0.2253305 0.1485773 2.045139e-02
## 1236 0.8684163 0.1446757 1.760001e-04
## 1242 0.3391096 0.1327166 4.389460e-04
## 1290 0.3391096 0.1327166 4.389460e-04
## 1291 0.3391096 0.1327166 4.389460e-04
## 86 0.1863252 0.1315144 9.273211e-04
## 948 0.3474957 0.1308481 6.092662e-04unlink("Mst1TG_young_and_old_dis_mitch.html")
mitch_report(res, outfile = "Mst1TG_young_and_old_dis_mitch.html")## Dataset saved as " /tmp/Rtmp0VANOs/Mst1TG_young_and_old_dis_mitch.rds ".##
##
## processing file: mitch.Rmd##
|
| | 0%
|
|.. | 3%
## inline R code fragments
##
##
|
|.... | 6%
## label: checklibraries (with options)
## List of 1
## $ echo: logi FALSE
##
##
|
|...... | 9%
## ordinary text without R code
##
##
|
|........ | 12%
## label: peek (with options)
## List of 1
## $ echo: logi FALSE
##
##
|
|.......... | 15%
## ordinary text without R code
##
##
|
|............ | 18%
## label: metrics (with options)
## List of 1
## $ echo: logi FALSE
##
##
|
|.............. | 21%
## ordinary text without R code
##
##
|
|................ | 24%
## label: scatterplot (with options)
## List of 5
## $ echo : logi FALSE
## $ fig.height: num 6
## $ fig.width : num 6.5
## $ message : logi FALSE
## $ warning : logi FALSE##
|
|................... | 26%
## ordinary text without R code
##
##
|
|..................... | 29%
## label: contourplot (with options)
## List of 5
## $ echo : logi FALSE
## $ fig.height: num 6
## $ fig.width : num 6.5
## $ warning : logi FALSE
## $ message : logi FALSE##
|
|....................... | 32%
## ordinary text without R code
##
##
|
|......................... | 35%
## label: input_geneset_metrics1 (with options)
## List of 2
## $ results: chr "asis"
## $ echo : logi FALSE
##
##
|
|........................... | 38%
## ordinary text without R code
##
##
|
|............................. | 41%
## label: input_geneset_metrics2 (with options)
## List of 5
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"##
|
|............................... | 44%
## ordinary text without R code
##
##
|
|................................. | 47%
## label: input_geneset_metrics3 (with options)
## List of 5
## $ results : chr "asis"
## $ echo : logi FALSE
## $ message : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7##
|
|................................... | 50%
## ordinary text without R code
##
##
|
|..................................... | 53%
## label: echart1d (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE
##
##
|
|....................................... | 56%
## label: echart2d (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE
##
##
|
|......................................... | 59%
## ordinary text without R code
##
##
|
|........................................... | 62%
## label: heatmap (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 10
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE##
|
|............................................. | 65%
## ordinary text without R code
##
##
|
|............................................... | 68%
## label: effectsize (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE
##
##
|
|................................................. | 71%
## ordinary text without R code
##
##
|
|................................................... | 74%
## label: results_table (with options)
## List of 2
## $ results: chr "asis"
## $ echo : logi FALSE
##
##
|
|...................................................... | 76%
## ordinary text without R code
##
##
|
|........................................................ | 79%
## label: results_table_complete (with options)
## List of 2
## $ results: chr "asis"
## $ echo : logi FALSE
##
##
|
|.......................................................... | 82%
## ordinary text without R code
##
##
|
|............................................................ | 85%
## label: detailed_geneset_reports1d (with options)
## List of 7
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 6
## $ fig.width : num 6
## $ out.width : chr "80%"
## $ comment : logi NA
## $ message : logi FALSE
##
##
|
|.............................................................. | 88%
## ordinary text without R code
##
##
|
|................................................................ | 91%
## label: detailed_geneset_reports2d (with options)
## List of 7
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 5
## $ fig.width : num 6
## $ out.width : chr "80%"
## $ comment : logi NA
## $ message : logi FALSE##
|
|.................................................................. | 94%
## ordinary text without R code
##
##
|
|.................................................................... | 97%
## label: session_info (with options)
## List of 3
## $ include: logi TRUE
## $ echo : logi TRUE
## $ results: chr "markup"
##
##
|
|......................................................................| 100%
## ordinary text without R code## output file: /mnt/bfx6/bfx/du_xiao/young_mst1tg/integrate/mitch.knit.md## /home/mdz/anaconda3/bin/pandoc +RTS -K512m -RTS /mnt/bfx6/bfx/du_xiao/young_mst1tg/integrate/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmp0VANOs/mitch_report.html --lua-filter /usr/lib/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/lib/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --standalone --section-divs --template /usr/lib/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header /tmp/Rtmp0VANOs/rmarkdown-str22934c80552d.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'##
## Output created: /tmp/Rtmp0VANOs/mitch_report.html## [1] TRUE# heatmaps of top sets by discordant size
topsets <- head(res$enrichment_result,50)$set
mytopsets <- gsets[which(names( gsets ) %in% topsets)]
i=1
par(mar = c(10, 8, 8, 4) + 0.2)
for ( i in seq_along(mytopsets) ) {
g <- as.vector(unlist(mytopsets[i]))
symbol <- sapply((strsplit(rownames(mx)," ")),"[[",2)
z <- mx[which(symbol %in% g),]
SETNAME = names(mytopsets[i])
heatmap.2( as.matrix(z), col = colfunc(25),scale = "row",
trace="none",margins = c(6,20), cexRow = .4, cexCol = .8)
mtext(SETNAME)
}
Custom gene set analysis
Run mitch with some hand-picked gene sets that are relevant to the Mst1 model.
# gene sets of interest
gsets <- gmt_import("../ref/pathways_of_interest_mouse.gmt")
# mitch pathways of interest
yy <- mitch_import(x, DEtype="deseq2", geneTable=gt)## Note: Mean no. genes in input = 17755## Note: no. genes in output = 14877## Note: estimated proportion of input genes in output = 0.838res <- mitch_calc(yy, gsets, priority="significance")## Note: When prioritising by significance (ie: small
## p-values), large effect sizes might be missed.head(res$enrichment_result,20)## set
## 24 The-citric-acid-(TCA)-cycle-and-respiratory-electron-transport
## 20 Respiratory-electron-transport
## 15 Mitochondrial-translation
## 13 Mitochondrial-protein-import
## 18 Pyruvate-metabolism-and-Citric-Acid-(TCA)-cycle
## 10 Mitochondrial-biogenesis
## 9 Mitochondrial-Fatty-Acid-Beta-Oxidation
## 5 Citric-acid-cycle-(TCA-cycle)
## 26 rRNA-processing-in-the-mitochondrion
## 2 Branched-chain-amino-acid-catabolism
## 14 Mitochondrial-tRNA-aminoacylation
## 25 Transcriptional-activation-of-mitochondrial-biogenesis
## 12 Mitochondrial-iron-sulfur-cluster-biogenesis
## 11 Mitochondrial-calcium-ion-transport
## 17 Oxygen-dependent-proline-hydroxylation-of-Hypoxia-inducible-Factor-Alpha
## 4 Cellular-response-to-hypoxia
## 22 Smooth-Muscle-Contraction
## 7 Glycolysis
## 21 Signaling-by-Hippo
## 16 Muscle-contraction
## setSize pMANOVA s.young s.old p.young p.old
## 24 167 1.252333e-82 -0.83525078 -0.81311829 5.140819e-78 5.461735e-74
## 20 100 4.626085e-57 -0.90358259 -0.85861000 2.801421e-55 4.761159e-50
## 15 94 6.954962e-44 -0.82536726 -0.75822286 1.108541e-43 4.243812e-37
## 13 57 8.672171e-23 -0.76190070 -0.68645027 2.285529e-23 2.947540e-19
## 18 51 4.483657e-21 -0.72496118 -0.76031508 3.153090e-19 5.373685e-21
## 10 88 1.702298e-19 -0.53042648 -0.55687581 7.776007e-18 1.670651e-19
## 9 31 5.132212e-17 -0.85843911 -0.84985203 1.245379e-16 2.491625e-16
## 5 22 2.511926e-13 -0.89428720 -0.88927511 3.711622e-13 5.015120e-13
## 26 22 1.564605e-11 -0.78311557 -0.85423335 2.002556e-10 3.928719e-12
## 2 19 5.851091e-11 -0.85859115 -0.87076252 9.044799e-11 4.893714e-11
## 14 19 3.662479e-08 -0.75631770 -0.71231518 1.135934e-08 7.591141e-08
## 25 51 3.864014e-08 -0.41798854 -0.46831084 2.427091e-07 7.229049e-09
## 12 10 6.993237e-05 -0.74099684 -0.77501850 4.948957e-05 2.191278e-05
## 11 21 1.528545e-04 -0.49488422 -0.50940457 8.639334e-05 5.318105e-05
## 17 60 4.598722e-04 -0.27615577 -0.16661267 2.172375e-04 2.569236e-02
## 4 68 8.973591e-04 -0.24792952 -0.14957121 4.101207e-04 3.305621e-02
## 22 31 9.211060e-03 0.03144107 0.21101807 7.619922e-01 4.206934e-02
## 7 63 1.433187e-02 -0.12364966 -0.20145251 8.984079e-02 5.713843e-03
## 21 20 1.540622e-02 0.37300263 0.30910682 3.883350e-03 1.672262e-02
## 16 148 2.975029e-02 -0.04379208 0.03414573 3.585713e-01 4.740819e-01
## s.dist SD p.adjustMANOVA
## 24 1.16567801 0.015650031 3.256067e-81
## 20 1.24646406 0.031800425 6.013911e-56
## 15 1.12077340 0.047478264 6.027634e-43
## 13 1.02552750 0.053351514 5.636911e-22
## 18 1.05054640 0.024998980 2.331501e-20
## 10 0.76906627 0.018702498 7.376623e-19
## 9 1.20795951 0.006071986 1.906250e-16
## 5 1.26117399 0.003544080 8.163761e-13
## 26 1.15887213 0.050287861 4.519969e-11
## 2 1.22286799 0.008606453 1.521284e-10
## 14 1.03894628 0.031114482 8.372031e-08
## 25 0.62771766 0.035583240 8.372031e-08
## 12 1.07225463 0.024056946 1.398647e-04
## 11 0.71021364 0.010267436 2.838726e-04
## 17 0.32252409 0.077458663 7.971118e-04
## 4 0.28955240 0.069549829 1.458209e-03
## 22 0.21334752 0.126980108 1.408750e-02
## 7 0.23637333 0.055014923 2.070159e-02
## 21 0.48443574 0.045181158 2.108219e-02
## 16 0.05553086 0.055110351 3.867538e-02unlink("Mst1TG_young_and_old_pathwayofinterest_mitch.html")
# top N gene heatmap
mitch_report(res, outfile = "Mst1TG_young_and_old_pathwayofinterest_mitch.html")## Dataset saved as " /tmp/Rtmp0VANOs/Mst1TG_young_and_old_pathwayofinterest_mitch.rds ".##
##
## processing file: mitch.Rmd##
|
| | 0%
|
|.. | 3%
## inline R code fragments
##
##
|
|.... | 6%
## label: checklibraries (with options)
## List of 1
## $ echo: logi FALSE
##
##
|
|...... | 9%
## ordinary text without R code
##
##
|
|........ | 12%
## label: peek (with options)
## List of 1
## $ echo: logi FALSE
##
##
|
|.......... | 15%
## ordinary text without R code
##
##
|
|............ | 18%
## label: metrics (with options)
## List of 1
## $ echo: logi FALSE
##
##
|
|.............. | 21%
## ordinary text without R code
##
##
|
|................ | 24%
## label: scatterplot (with options)
## List of 5
## $ echo : logi FALSE
## $ fig.height: num 6
## $ fig.width : num 6.5
## $ message : logi FALSE
## $ warning : logi FALSE##
|
|................... | 26%
## ordinary text without R code
##
##
|
|..................... | 29%
## label: contourplot (with options)
## List of 5
## $ echo : logi FALSE
## $ fig.height: num 6
## $ fig.width : num 6.5
## $ warning : logi FALSE
## $ message : logi FALSE##
|
|....................... | 32%
## ordinary text without R code
##
##
|
|......................... | 35%
## label: input_geneset_metrics1 (with options)
## List of 2
## $ results: chr "asis"
## $ echo : logi FALSE
##
##
|
|........................... | 38%
## ordinary text without R code
##
##
|
|............................. | 41%
## label: input_geneset_metrics2 (with options)
## List of 5
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"##
|
|............................... | 44%
## ordinary text without R code
##
##
|
|................................. | 47%
## label: input_geneset_metrics3 (with options)
## List of 5
## $ results : chr "asis"
## $ echo : logi FALSE
## $ message : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7##
|
|................................... | 50%
## ordinary text without R code
##
##
|
|..................................... | 53%
## label: echart1d (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE
##
##
|
|....................................... | 56%
## label: echart2d (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE
##
##
|
|......................................... | 59%
## ordinary text without R code
##
##
|
|........................................... | 62%
## label: heatmap (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 10
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE##
|
|............................................. | 65%
## ordinary text without R code
##
##
|
|............................................... | 68%
## label: effectsize (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE
##
##
|
|................................................. | 71%
## ordinary text without R code
##
##
|
|................................................... | 74%
## label: results_table (with options)
## List of 2
## $ results: chr "asis"
## $ echo : logi FALSE
##
##
|
|...................................................... | 76%
## ordinary text without R code
##
##
|
|........................................................ | 79%
## label: results_table_complete (with options)
## List of 2
## $ results: chr "asis"
## $ echo : logi FALSE
##
##
|
|.......................................................... | 82%
## ordinary text without R code
##
##
|
|............................................................ | 85%
## label: detailed_geneset_reports1d (with options)
## List of 7
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 6
## $ fig.width : num 6
## $ out.width : chr "80%"
## $ comment : logi NA
## $ message : logi FALSE
##
##
|
|.............................................................. | 88%
## ordinary text without R code
##
##
|
|................................................................ | 91%
## label: detailed_geneset_reports2d (with options)
## List of 7
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 5
## $ fig.width : num 6
## $ out.width : chr "80%"
## $ comment : logi NA
## $ message : logi FALSE##
|
|.................................................................. | 94%
## ordinary text without R code
##
##
|
|.................................................................... | 97%
## label: session_info (with options)
## List of 3
## $ include: logi TRUE
## $ echo : logi TRUE
## $ results: chr "markup"
##
##
|
|......................................................................| 100%
## ordinary text without R code## output file: /mnt/bfx6/bfx/du_xiao/young_mst1tg/integrate/mitch.knit.md## /home/mdz/anaconda3/bin/pandoc +RTS -K512m -RTS /mnt/bfx6/bfx/du_xiao/young_mst1tg/integrate/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmp0VANOs/mitch_report.html --lua-filter /usr/lib/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/lib/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --standalone --section-divs --template /usr/lib/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header /tmp/Rtmp0VANOs/rmarkdown-str2293779f612.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'##
## Output created: /tmp/Rtmp0VANOs/mitch_report.html## [1] TRUE# heatmaps of pathways of interest
# colour scheme
colfunc <- colorRampPalette(c("blue", "white", "red"))
topsets <- head(res$enrichment_result,50)$set
mytopsets <- gsets[which(names( gsets ) %in% topsets)]
yo <- young[,7:ncol(young)]
colnames(yo) <- paste("y",colnames(yo))
ol <- old[,7:ncol(old)]
colnames(ol) <- paste("o",colnames(ol))
mx <- merge(yo,ol,by=0)
rownames(mx) <- mx$Row.names
mx$Row.names = NULL
i = 1
par(mar = c(10, 8, 8, 4) + 0.2)
for ( i in seq_along(mytopsets) ) {
g <- as.vector(unlist(mytopsets[i]))
symbol <- sapply((strsplit(rownames(mx)," ")),"[[",2)
z <- mx[which(symbol %in% g),]
SETNAME=names(mytopsets[i])
heatmap.2( as.matrix(z), col=colfunc(25),scale="row",
trace="none",margins = c(6,20), cexRow=.4, cexCol=.8)
mtext(SETNAME)
}
Mitochondrial complexes
mt <- gmt_import("../ref/mt_complexes_mouse.gmt")
# have a look and check the gene names are correct
mt## $`Complex-1`
## [1] "1700029P11Rik" "mt-Nd1" "mt-Nd2" "mt-Nd3"
## [5] "mt-Nd4" "mt-Nd4l" "mt-Nd5" "mt-Nd6"
## [9] "Ndufa1" "Ndufa10" "Ndufa11" "Ndufa12"
## [13] "Ndufa13" "Ndufa2" "Ndufa3" "Ndufa5"
## [17] "Ndufa6" "Ndufa7" "Ndufa8" "Ndufa9"
## [21] "Ndufab1" "Ndufb10" "Ndufb1-ps" "Ndufb2"
## [25] "Ndufb3" "Ndufb4" "Ndufb5" "Ndufb6"
## [29] "Ndufb7" "Ndufb8" "Ndufb9" "Ndufc1"
## [33] "Ndufc2" "Ndufs1" "Ndufs2" "Ndufs3"
## [37] "Ndufs4" "Ndufs5" "Ndufs6" "Ndufs7"
## [41] "Ndufs8" "Ndufv1" "Ndufv2" "Ndufv3"
##
## $`Complex-1-Assembly-Factors`
## [1] "Acad9" "Ecsit" "Foxred1" "Ndufaf1" "Ndufaf2" "Ndufaf4"
## [7] "Ndufaf5" "Ndufaf6" "Ndufaf7" "Ndufaf8" "Nubpl" "Timmdc1"
## [13] "Tmem126b"
##
## $`Complex-2`
## [1] "Sdha" "Sdhb" "Sdhc" "Sdhd"
##
## $`Complex-2-Assembly-Factors`
## [1] "Sdhaf1" "Sdhaf2" "Sdhaf3" "Sdhaf4"
##
## $`Complex-3`
## [1] "Cyc1" "mt-Cytb" "Uqcr10" "Uqcr11" "Uqcrb" "Uqcrc1" "Uqcrc2"
## [8] "Uqcrfs1" "Uqcrq"
##
## $`Complex-3-Assembly-Factors`
## [1] "Bcs1l" "Lyrm7" "Ptcd2" "Ttc19" "Uqcc1" "Uqcc2" "Uqcc3"
##
## $`Complex-4`
## [1] "Cox5a" "Cox5b" "Cox6c" "Cox7b" "Cox7c" "mt-Co1" "mt-Co2" "mt-Co3"
##
## $`Complex-4-Assembly-Factors`
## [1] "Apopt1" "Cep89" "Coa3" "Coa4" "Coa5" "Coa6" "Coa7"
## [8] "Cox10" "Cox11" "Cox14" "Cox16" "Cox18" "Cox19" "Cox20"
## [15] "Fastkd2" "Gm21987" "Lrpprc" "Ndufa4" "Oxa1l" "Pet100" "Pet117"
## [22] "Sco1" "Sco2" "Surf1" "Taco1"
##
## $`Complex-5`
## [1] "Atp5a1" "Atp5b" "Atp5c1" "Atp5d" "Atp5e" "Atp5g3" "Atp5h"
## [8] "Atp5j" "Atp5j2" "Atp5k" "Atp5l" "Atp5o" "Atp5pb" "mt-Atp6"
## [15] "mt-Atp8"
##
## $`Complex-5-Assembly-Factors`
## [1] "Atpaf1" "Atpaf2" "Tmem70"
##
## attr(,"originfile")
## [1] "../ref/mt_complexes_mouse.gmt"# mitch pathways of interest
res <- mitch_calc(yy, mt, priority="effect",minsetsize=3)## Note: Enrichments with large effect sizes may not be
## statistically significant.head(res$enrichment_result,20)## set setSize pMANOVA s.young s.old
## 3 Complex-2 4 1.630452e-03 -0.9933773 -0.9735090
## 7 Complex-4 8 7.489554e-06 -0.9618838 -0.9204889
## 1 Complex-1 43 5.682735e-28 -0.9484747 -0.9254259
## 5 Complex-3 9 2.035360e-06 -0.9607360 -0.9060473
## 9 Complex-5 15 4.962915e-10 -0.9358364 -0.9197416
## 10 Complex-5-Assembly-Factors 3 1.395221e-02 -0.9142575 -0.9381023
## 2 Complex-1-Assembly-Factors 13 2.965384e-07 -0.8456363 -0.8233419
## 4 Complex-2-Assembly-Factors 4 1.885567e-02 -0.8053184 -0.7200968
## 6 Complex-3-Assembly-Factors 7 2.810338e-03 -0.7364204 -0.6735325
## 8 Complex-4-Assembly-Factors 23 7.371441e-07 -0.6348575 -0.5616581
## p.young p.old s.dist SD p.adjustMANOVA
## 3 5.793699e-04 7.455891e-04 1.3908696 0.01404895 2.329217e-03
## 7 2.448833e-06 6.500947e-06 1.3313603 0.02927058 1.248259e-05
## 1 4.414790e-27 7.427705e-26 1.3251481 0.01629801 5.682735e-27
## 5 5.966715e-07 2.502900e-06 1.3205814 0.03867073 4.070720e-06
## 9 3.424155e-10 6.823345e-10 1.3121411 0.01138070 2.481457e-09
## 10 6.095260e-03 4.890470e-03 1.3099247 0.01686078 1.550245e-02
## 2 1.286773e-07 2.727380e-07 1.1802511 0.01576455 9.884612e-07
## 4 5.279602e-03 1.262398e-02 1.0803134 0.06026073 1.885567e-02
## 6 7.401164e-04 2.028537e-03 0.9979785 0.04446845 3.512922e-03
## 8 1.353405e-07 3.113497e-06 0.8476461 0.05175981 1.842860e-06unlink("Mst1TG_young_and_old_mitocomplex_mitch.html")
# top N gene heatmap
mitch_report(res, outfile = "Mst1TG_young_and_old_mitocomplex_mitch.html")## Dataset saved as " /tmp/Rtmp0VANOs/Mst1TG_young_and_old_mitocomplex_mitch.rds ".##
##
## processing file: mitch.Rmd##
|
| | 0%
|
|.. | 3%
## inline R code fragments
##
##
|
|.... | 6%
## label: checklibraries (with options)
## List of 1
## $ echo: logi FALSE
##
##
|
|...... | 9%
## ordinary text without R code
##
##
|
|........ | 12%
## label: peek (with options)
## List of 1
## $ echo: logi FALSE
##
##
|
|.......... | 15%
## ordinary text without R code
##
##
|
|............ | 18%
## label: metrics (with options)
## List of 1
## $ echo: logi FALSE
##
##
|
|.............. | 21%
## ordinary text without R code
##
##
|
|................ | 24%
## label: scatterplot (with options)
## List of 5
## $ echo : logi FALSE
## $ fig.height: num 6
## $ fig.width : num 6.5
## $ message : logi FALSE
## $ warning : logi FALSE##
|
|................... | 26%
## ordinary text without R code
##
##
|
|..................... | 29%
## label: contourplot (with options)
## List of 5
## $ echo : logi FALSE
## $ fig.height: num 6
## $ fig.width : num 6.5
## $ warning : logi FALSE
## $ message : logi FALSE##
|
|....................... | 32%
## ordinary text without R code
##
##
|
|......................... | 35%
## label: input_geneset_metrics1 (with options)
## List of 2
## $ results: chr "asis"
## $ echo : logi FALSE
##
##
|
|........................... | 38%
## ordinary text without R code
##
##
|
|............................. | 41%
## label: input_geneset_metrics2 (with options)
## List of 5
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"##
|
|............................... | 44%
## ordinary text without R code
##
##
|
|................................. | 47%
## label: input_geneset_metrics3 (with options)
## List of 5
## $ results : chr "asis"
## $ echo : logi FALSE
## $ message : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7##
|
|................................... | 50%
## ordinary text without R code
##
##
|
|..................................... | 53%
## label: echart1d (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE
##
##
|
|....................................... | 56%
## label: echart2d (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE
##
##
|
|......................................... | 59%
## ordinary text without R code
##
##
|
|........................................... | 62%
## label: heatmap (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 10
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE##
|
|............................................. | 65%
## ordinary text without R code
##
##
|
|............................................... | 68%
## label: effectsize (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE
##
##
|
|................................................. | 71%
## ordinary text without R code
##
##
|
|................................................... | 74%
## label: results_table (with options)
## List of 2
## $ results: chr "asis"
## $ echo : logi FALSE
##
##
|
|...................................................... | 76%
## ordinary text without R code
##
##
|
|........................................................ | 79%
## label: results_table_complete (with options)
## List of 2
## $ results: chr "asis"
## $ echo : logi FALSE
##
##
|
|.......................................................... | 82%
## ordinary text without R code
##
##
|
|............................................................ | 85%
## label: detailed_geneset_reports1d (with options)
## List of 7
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 6
## $ fig.width : num 6
## $ out.width : chr "80%"
## $ comment : logi NA
## $ message : logi FALSE
##
##
|
|.............................................................. | 88%
## ordinary text without R code
##
##
|
|................................................................ | 91%
## label: detailed_geneset_reports2d (with options)
## List of 7
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 5
## $ fig.width : num 6
## $ out.width : chr "80%"
## $ comment : logi NA
## $ message : logi FALSE##
|
|.................................................................. | 94%
## ordinary text without R code
##
##
|
|.................................................................... | 97%
## label: session_info (with options)
## List of 3
## $ include: logi TRUE
## $ echo : logi TRUE
## $ results: chr "markup"
##
##
|
|......................................................................| 100%
## ordinary text without R code## output file: /mnt/bfx6/bfx/du_xiao/young_mst1tg/integrate/mitch.knit.md## /home/mdz/anaconda3/bin/pandoc +RTS -K512m -RTS /mnt/bfx6/bfx/du_xiao/young_mst1tg/integrate/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmp0VANOs/mitch_report.html --lua-filter /usr/lib/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/lib/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --standalone --section-divs --template /usr/lib/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header /tmp/Rtmp0VANOs/rmarkdown-str229334f36ae8.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'##
## Output created: /tmp/Rtmp0VANOs/mitch_report.html## [1] TRUEmytopsets <- head(res$enrichment_result,50)$set
i = 1
par(mar = c(10, 8, 8, 4) + 0.2)
for ( i in seq_along(mt) ) {
g <- as.vector(unlist(mt[i]))
symbol <- sapply((strsplit(rownames(mx)," ")),"[[",2)
z <- mx[which(symbol %in% g),]
SETNAME=names(mt)[i]
heatmap.2( as.matrix(z), col=colfunc(25),scale="row",
trace="none",margins = c(6,20), cexRow=.8, cexCol=.8)
mtext(SETNAME)
}
# now 1D mitch for young and old to create beeswarm charts
yy2 <- yy[,1,drop=FALSE]
res <- mitch_calc(yy2, mt, priority="effect",minsetsize=3)## Note: Enrichments with large effect sizes may not be
## statistically significant.head(res$enrichment_result,20)## set setSize pANOVA s.dist p.adjustANOVA
## 3 Complex-2 4 5.793699e-04 -0.9933773 8.276713e-04
## 7 Complex-4 8 2.448833e-06 -0.9618838 4.081389e-06
## 5 Complex-3 9 5.966715e-07 -0.9607360 1.193343e-06
## 1 Complex-1 43 4.414790e-27 -0.9484747 4.414790e-26
## 9 Complex-5 15 3.424155e-10 -0.9358364 1.712077e-09
## 10 Complex-5-Assembly-Factors 3 6.095260e-03 -0.9142575 6.095260e-03
## 2 Complex-1-Assembly-Factors 13 1.286773e-07 -0.8456363 3.383513e-07
## 4 Complex-2-Assembly-Factors 4 5.279602e-03 -0.8053184 5.866225e-03
## 6 Complex-3-Assembly-Factors 7 7.401164e-04 -0.7364204 9.251456e-04
## 8 Complex-4-Assembly-Factors 23 1.353405e-07 -0.6348575 3.383513e-07unlink("Mst1TG_young_mitocomplex_mitch.html")
mitch_report(res, outfile = "Mst1TG_young_mitocomplex_mitch.html")## Dataset saved as " /tmp/Rtmp0VANOs/Mst1TG_young_mitocomplex_mitch.rds ".
##
##
## processing file: mitch.Rmd##
|
| | 0%
|
|.. | 3%
## inline R code fragments
##
##
|
|.... | 6%
## label: checklibraries (with options)
## List of 1
## $ echo: logi FALSE
##
##
|
|...... | 9%
## ordinary text without R code
##
##
|
|........ | 12%
## label: peek (with options)
## List of 1
## $ echo: logi FALSE
##
##
|
|.......... | 15%
## ordinary text without R code
##
##
|
|............ | 18%
## label: metrics (with options)
## List of 1
## $ echo: logi FALSE
##
##
|
|.............. | 21%
## ordinary text without R code
##
##
|
|................ | 24%
## label: scatterplot (with options)
## List of 5
## $ echo : logi FALSE
## $ fig.height: num 6
## $ fig.width : num 6.5
## $ message : logi FALSE
## $ warning : logi FALSE##
|
|................... | 26%
## ordinary text without R code
##
##
|
|..................... | 29%
## label: contourplot (with options)
## List of 5
## $ echo : logi FALSE
## $ fig.height: num 6
## $ fig.width : num 6.5
## $ warning : logi FALSE
## $ message : logi FALSE## Contour plot does not apply to unidimensional analysis.##
|
|....................... | 32%
## ordinary text without R code
##
##
|
|......................... | 35%
## label: input_geneset_metrics1 (with options)
## List of 2
## $ results: chr "asis"
## $ echo : logi FALSE
##
##
|
|........................... | 38%
## ordinary text without R code
##
##
|
|............................. | 41%
## label: input_geneset_metrics2 (with options)
## List of 5
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"##
|
|............................... | 44%
## ordinary text without R code
##
##
|
|................................. | 47%
## label: input_geneset_metrics3 (with options)
## List of 5
## $ results : chr "asis"
## $ echo : logi FALSE
## $ message : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7##
|
|................................... | 50%
## ordinary text without R code
##
##
|
|..................................... | 53%
## label: echart1d (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE
##
##
|
|....................................... | 56%
## label: echart2d (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE
##
##
|
|......................................... | 59%
## ordinary text without R code
##
##
|
|........................................... | 62%
## label: heatmap (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 10
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE
##
##
|
|............................................. | 65%
## ordinary text without R code
##
##
|
|............................................... | 68%
## label: effectsize (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE
##
##
|
|................................................. | 71%
## ordinary text without R code
##
##
|
|................................................... | 74%
## label: results_table (with options)
## List of 2
## $ results: chr "asis"
## $ echo : logi FALSE
##
##
|
|...................................................... | 76%
## ordinary text without R code
##
##
|
|........................................................ | 79%
## label: results_table_complete (with options)
## List of 2
## $ results: chr "asis"
## $ echo : logi FALSE
##
##
|
|.......................................................... | 82%
## ordinary text without R code
##
##
|
|............................................................ | 85%
## label: detailed_geneset_reports1d (with options)
## List of 7
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 6
## $ fig.width : num 6
## $ out.width : chr "80%"
## $ comment : logi NA
## $ message : logi FALSE##
|
|.............................................................. | 88%
## ordinary text without R code
##
##
|
|................................................................ | 91%
## label: detailed_geneset_reports2d (with options)
## List of 7
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 5
## $ fig.width : num 6
## $ out.width : chr "80%"
## $ comment : logi NA
## $ message : logi FALSE
##
##
|
|.................................................................. | 94%
## ordinary text without R code
##
##
|
|.................................................................... | 97%
## label: session_info (with options)
## List of 3
## $ include: logi TRUE
## $ echo : logi TRUE
## $ results: chr "markup"
##
##
|
|......................................................................| 100%
## ordinary text without R code## output file: /mnt/bfx6/bfx/du_xiao/young_mst1tg/integrate/mitch.knit.md## /home/mdz/anaconda3/bin/pandoc +RTS -K512m -RTS /mnt/bfx6/bfx/du_xiao/young_mst1tg/integrate/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmp0VANOs/mitch_report.html --lua-filter /usr/lib/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/lib/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --standalone --section-divs --template /usr/lib/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header /tmp/Rtmp0VANOs/rmarkdown-str22937e586c7b.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'##
## Output created: /tmp/Rtmp0VANOs/mitch_report.html## [1] TRUEyy3 <- yy[,2,drop=FALSE]
res <- mitch_calc(yy3, mt, priority="effect",minsetsize=3)## Note: Enrichments with large effect sizes may not be
## statistically significant.head(res$enrichment_result,20)## set setSize pANOVA s.dist p.adjustANOVA
## 3 Complex-2 4 7.455891e-04 -0.9735090 1.065127e-03
## 10 Complex-5-Assembly-Factors 3 4.890470e-03 -0.9381023 5.433856e-03
## 1 Complex-1 43 7.427705e-26 -0.9254259 7.427705e-25
## 7 Complex-4 8 6.500947e-06 -0.9204889 1.083491e-05
## 9 Complex-5 15 6.823345e-10 -0.9197416 3.411672e-09
## 5 Complex-3 9 2.502900e-06 -0.9060473 6.226995e-06
## 2 Complex-1-Assembly-Factors 13 2.727380e-07 -0.8233419 9.091267e-07
## 4 Complex-2-Assembly-Factors 4 1.262398e-02 -0.7200968 1.262398e-02
## 6 Complex-3-Assembly-Factors 7 2.028537e-03 -0.6735325 2.535671e-03
## 8 Complex-4-Assembly-Factors 23 3.113497e-06 -0.5616581 6.226995e-06unlink("Mst1TG_old_mitocomplex_mitch.html")
mitch_report(res, outfile = "Mst1TG_old_mitocomplex_mitch.html")## Dataset saved as " /tmp/Rtmp0VANOs/Mst1TG_old_mitocomplex_mitch.rds ".
##
##
## processing file: mitch.Rmd##
|
| | 0%
|
|.. | 3%
## inline R code fragments
##
##
|
|.... | 6%
## label: checklibraries (with options)
## List of 1
## $ echo: logi FALSE
##
##
|
|...... | 9%
## ordinary text without R code
##
##
|
|........ | 12%
## label: peek (with options)
## List of 1
## $ echo: logi FALSE
##
##
|
|.......... | 15%
## ordinary text without R code
##
##
|
|............ | 18%
## label: metrics (with options)
## List of 1
## $ echo: logi FALSE
##
##
|
|.............. | 21%
## ordinary text without R code
##
##
|
|................ | 24%
## label: scatterplot (with options)
## List of 5
## $ echo : logi FALSE
## $ fig.height: num 6
## $ fig.width : num 6.5
## $ message : logi FALSE
## $ warning : logi FALSE##
|
|................... | 26%
## ordinary text without R code
##
##
|
|..................... | 29%
## label: contourplot (with options)
## List of 5
## $ echo : logi FALSE
## $ fig.height: num 6
## $ fig.width : num 6.5
## $ warning : logi FALSE
## $ message : logi FALSE## Contour plot does not apply to unidimensional analysis.##
|
|....................... | 32%
## ordinary text without R code
##
##
|
|......................... | 35%
## label: input_geneset_metrics1 (with options)
## List of 2
## $ results: chr "asis"
## $ echo : logi FALSE
##
##
|
|........................... | 38%
## ordinary text without R code
##
##
|
|............................. | 41%
## label: input_geneset_metrics2 (with options)
## List of 5
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"##
|
|............................... | 44%
## ordinary text without R code
##
##
|
|................................. | 47%
## label: input_geneset_metrics3 (with options)
## List of 5
## $ results : chr "asis"
## $ echo : logi FALSE
## $ message : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7##
|
|................................... | 50%
## ordinary text without R code
##
##
|
|..................................... | 53%
## label: echart1d (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE
##
##
|
|....................................... | 56%
## label: echart2d (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE
##
##
|
|......................................... | 59%
## ordinary text without R code
##
##
|
|........................................... | 62%
## label: heatmap (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 10
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE
##
##
|
|............................................. | 65%
## ordinary text without R code
##
##
|
|............................................... | 68%
## label: effectsize (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE
##
##
|
|................................................. | 71%
## ordinary text without R code
##
##
|
|................................................... | 74%
## label: results_table (with options)
## List of 2
## $ results: chr "asis"
## $ echo : logi FALSE
##
##
|
|...................................................... | 76%
## ordinary text without R code
##
##
|
|........................................................ | 79%
## label: results_table_complete (with options)
## List of 2
## $ results: chr "asis"
## $ echo : logi FALSE
##
##
|
|.......................................................... | 82%
## ordinary text without R code
##
##
|
|............................................................ | 85%
## label: detailed_geneset_reports1d (with options)
## List of 7
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 6
## $ fig.width : num 6
## $ out.width : chr "80%"
## $ comment : logi NA
## $ message : logi FALSE##
|
|.............................................................. | 88%
## ordinary text without R code
##
##
|
|................................................................ | 91%
## label: detailed_geneset_reports2d (with options)
## List of 7
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 5
## $ fig.width : num 6
## $ out.width : chr "80%"
## $ comment : logi NA
## $ message : logi FALSE
##
##
|
|.................................................................. | 94%
## ordinary text without R code
##
##
|
|.................................................................... | 97%
## label: session_info (with options)
## List of 3
## $ include: logi TRUE
## $ echo : logi TRUE
## $ results: chr "markup"
##
##
|
|......................................................................| 100%
## ordinary text without R code## output file: /mnt/bfx6/bfx/du_xiao/young_mst1tg/integrate/mitch.knit.md## /home/mdz/anaconda3/bin/pandoc +RTS -K512m -RTS /mnt/bfx6/bfx/du_xiao/young_mst1tg/integrate/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmp0VANOs/mitch_report.html --lua-filter /usr/lib/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/lib/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --standalone --section-divs --template /usr/lib/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header /tmp/Rtmp0VANOs/rmarkdown-str229329eb6a54.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'##
## Output created: /tmp/Rtmp0VANOs/mitch_report.html
## [1] TRUELipid custom gene set analysis
Biosynthesis and transport.
Downloaded from MGI:
lipid_biosynth <- c("9130409I23Rik", "A3galt2", "A4galt", "Abca2", "Abca3", "Abca8a", "Abca8b", "Abcd1", "Abcd2", "Abcd3", "Abcg1", "Abcg4",
"Abhd2", "Abhd3", "Abhd4", "Abhd5", "Abhd6", "Abhd8", "Acaca", "Acacb", "Acadl", "Acadvl", "Acat1", "Acbd3", "Acer1", "Acer2", "Acer3",
"Acly", "Acot7", "Acsbg1", "Acsbg2", "Acsbg3", "Acsf3", "Acsl1", "Acsl3", "Acsl4", "Acsl5", "Acsl6", "Acsm1", "Acsm2", "Acsm3", "Acsm4",
"Acsm5", "Acss1", "Acss2", "Adgrf5", "Adora2b", "Agk", "Agmo", "Agpat1", "Agpat2", "Agpat3", "Agpat4", "Agpat5", "Agps", "Agt", "Ajuba",
"Akr1c18", "Akr1c20", "Akr1c21", "Akr1c6", "Akr1d1", "Akt1", "Aldh1a1", "Aldh1a2", "Aldh1a3", "Aldh8a1", "Alox12", "Alox12b", "Alox12e",
"Alox15", "Alox5", "Alox8", "Aloxe3", "Amacr", "Ang", "Ang2", "Ang3", "Ang4", "Ang6", "Anxa1", "Apoa1", "Apoa2", "Apoa4", "Apoa5", "Apob",
"Apoc1", "Apoc2", "Apoc2l", "Apoc3", "Apoe", "Armc5", "Asah1", "Asah2", "Asxl3", "Atg14", "Atg7", "Atp1a1", "Avil", "Avp", "Avpr1a", "Awat2",
"B3galt1", "B3galt2", "B3galt4", "B3gnt5", "B4galnt1", "B4galt3", "B4galt4", "B4galt5", "B4galt6", "Baat", "Becn1", "Bmp2", "Bmp5", "Bmp6",
"Bmpr1b", "Bpnt1", "Bpnt2", "Brca1", "Bscl2", "C3", "Cacna1h", "Capn2", "Cbr4", "Ccdc3", "Ccn1", "Cd74", "Cdipt", "Cdk4", "Cds1", "Cds2",
"Ceacam1", "Ceacam2", "Cept1", "Cerkl", "Cers1", "Cers2", "Cers3", "Cers4", "Cers5", "Cers6", "Ces1a", "Ces1b", "Ces1c", "Ces1d", "Ces1e",
"Ces1f", "Ces1g", "Cftr", "Cga", "Ch25h", "Chka", "Chkb", "Chp1", "Chpt1", "Cish", "Clcn2", "Cln3", "Cmtm2a", "Cnep1r1", "Coq2", "Creb1",
"Crebl2", "Crh", "Crls1", "Crppa", "Ctdnep1", "Cwh43", "Cyb5r1", "Cyb5r2", "Cyb5r3", "Cyp11a1", "Cyp11b1", "Cyp11b2", "Cyp17a1", "Cyp19a1",
"Cyp1a1", "Cyp21a1", "Cyp27a1", "Cyp27b1", "Cyp2r1", "Cyp39a1", "Cyp4f39", "Cyp51", "Cyp7a1", "Cyp7b1", "Cyp8b1", "Dab2", "Daglb", "Dbi",
"Dctn6", "Ddx20", "Decr2", "Degs1", "Degs2", "Dgat1", "Dgat2", "Dgat2l6", "Dgka", "Dgkb", "Dgkd", "Dgke", "Dgkg", "Dgkh", "Dgki", "Dgkq",
"Dgkz", "Dhcr24", "Dhcr7", "Dhdds", "Dhh", "Dhrs11", "Dhrs7b", "Dhrs9", "Dkk3", "Dkkl1", "Dolk", "Dolpp1", "Dpm1", "Dpm2", "Dpm3", "Ebp",
"Edn1", "Edn2", "Efr3b", "Egr1", "Eif6", "Elovl1", "Elovl2", "Elovl3", "Elovl4", "Elovl5", "Elovl6", "Elovl7", "Enpp7", "Erbb4", "Erg28",
"Erlin1", "Erlin2", "Etnk1", "Etnk2", "Fa2h", "Fabp3", "Fabp5", "Fads1", "Fads2", "Fads2b", "Fads3", "Fads6", "Fam126a", "Fam126b", "Fam3a",
"Far1", "Fasn", "Fdft1", "Fdps", "Fdx1", "Fgf1", "Fgf15", "Fgf2", "Fgf7", "Fgfr4", "Fitm1", "Fitm2", "Fshb", "Fut4", "Fut9", "G6pd2", "G6pdx",
"Gal3st1", "Gal3st3", "Gba", "Gfi1", "Ggps1", "Gh", "Gip", "Gm12248", "Gm20671", "Gm28778", "Gm44502", "Gm6993", "Gm9745", "Gnpat", "Gpaa1",
"Gpam", "Gpat2", "Gpat3", "Gpat4", "Gper1", "Gpld1", "Gstm4", "Gstm7", "Gstp1", "Gstp2", "H2-Ke6", "H6pd", "Hacd1", "Hacd2", "Hacd3", "Hacd4",
"Hdhd5", "Hexb", "Hint2", "Hmgcr", "Hmgcs1", "Hmgcs2", "Hnf1a", "Hnf4a", "Hpgds", "Hrh1", "Hsd11b1", "Hsd17b1", "Hsd17b10", "Hsd17b11",
"Hsd17b12", "Hsd17b13", "Hsd17b2", "Hsd17b3", "Hsd17b7", "Hsd3b1", "Hsd3b2", "Hsd3b3", "Hsd3b4", "Hsd3b5", "Hsd3b6", "Hsd3b7", "Hsd3b9",
"Htr2a", "Htr2b", "Htr2c", "Idh1", "Idi1", "Idi2", "Ifng", "Igf1", "Igf1r", "Igf2", "Igfbp7", "Il1a", "Il1b", "Impa1", "Impa2", "Inpp1",
"Inpp4b", "Inppl1", "Insig1", "Insig2", "Ip6k1", "Ip6k2", "Ip6k3", "Isyna1", "Itpka", "Itpkb", "Itpkc", "Kdsr", "Lbr", "Lcat", "Lclat1", "Ldlr",
"Lep", "Lhcgr", "Lias", "Lipc", "Lipg", "Liph", "Lipi", "Lpcat1", "Lpcat2", "Lpcat2b", "Lpcat3", "Lpcat4", "Lpgat1", "Lpin1", "Lpin2", "Lpin3",
"Lpl", "Lss", "Ltc4s", "Malrd1", "Mapk9", "Mboat1", "Mboat2", "Mboat7", "Mcat", "Mecr", "Med1", "Mfsd2a", "Mgll", "Mid1ip1", "Mif", "Mlxipl",
"Mlycd", "Mogat1", "Mogat2", "Mppe1", "Msmo1", "Mtor", "Mup1", "Mvd", "Mvk", "Myo5a", "Ndufab1", "Nfkb1", "Npc1l1", "Nr0b1", "Nr1d1", "Nr1h2",
"Nr1h3", "Nr1h4", "Nr3c1", "Nsdhl", "Nus1", "Obp2a", "Olah", "Ormdl1", "Ormdl2", "Ormdl3", "Osbp", "Oxsm", "P2rx1", "P2rx7", "P3r3urf", "Pam",
"Pbx1", "Pck1", "Pck2", "Pcx", "Pcyt1a", "Pcyt1b", "Pcyt2", "Pde8b", "Pdgfa", "Pdgfb", "Pdk4", "Pdss1", "Pdss2", "Pecr", "Peds1", "Pemt",
"Pex2", "Pex5", "Pex7", "Pgap1", "Pgap2", "Pgap3", "Pgap4", "Pgs1", "Pi4k2a", "Pi4k2b", "Pi4ka", "Pi4kb", "Pibf1", "Piga", "Pigb", "Pigc",
"Pigf", "Pigg", "Pigh", "Pigk", "Pigl", "Pigm", "Pign", "Pigo", "Pigp", "Pigq", "Pigs", "Pigt", "Pigu", "Pigv", "Pigw", "Pigx", "Pigyl", "Pigz",
"Pik3c2a", "Pik3c2b", "Pik3c2g", "Pik3c3", "Pik3ca", "Pik3cb", "Pik3cd", "Pik3cg", "Pik3r1", "Pik3r2", "Pik3r3", "Pik3r4", "Pip4k2a", "Pip4k2b",
"Pip4k2c", "Pip5k1a", "Pip5k1b", "Pip5k1c", "Pip5kl1", "Pisd", "Pla2g10", "Pla2g15", "Pla2g1b", "Pla2g3", "Pla2g4a", "Pla2g4c", "Pla2g4f",
"Pla2g5", "Pla2g6", "Plaat3", "Plce1", "Plcg2", "Pld1", "Pld2", "Plin5", "Plp1", "Plpp1", "Plscr1", "Plscr3", "Pmvk", "Pnpla1", "Pnpla2",
"Pnpla3", "Pnpla8", "Por", "Ppara", "Ppard", "Ppargc1a", "Prkaa1", "Prkaa2", "Prkab1", "Prkab2", "Prkag1", "Prkag2", "Prkag3", "Prkcd", "Prmt3",
"Prox1", "Prpf19", "Prxl2b", "Ptdss1", "Ptdss2", "Ptgds", "Ptges", "Ptges2", "Ptges3", "Ptgis", "Ptgs1", "Ptgs2", "Ptpmt1", "Pyurf", "Qk",
"Rab38", "Rbp1", "Rdh1", "Rdh10", "Rdh16", "Rdh16f2", "Rdh19", "Rdh9", "Rest", "Rgn", "Rpe65", "Samd8", "Sc5d", "Scap", "Scarb1", "Sccpdh",
"Scd1", "Scd2", "Scd3", "Scd4", "Sco1", "Scp2", "Scp2d1", "Sdr42e1", "Sec14l2", "Selenoi", "Serac1", "Serinc1", "Serinc4", "Serinc5",
"Serpina12", "Sf1", "Sgms1", "Sgms2", "Sh3glb1", "Sh3yl1", "Sik1", "Sirt1", "Sirt3", "Sirt4", "Sla2", "Slc27a1", "Slc27a2", "Slc27a5", "Slc45a3",
"Smg1", "Smpd1", "Smpd2", "Smpd3", "Smpd4", "Smpd5", "Snai1", "Snai2", "Socs1", "Socs2", "Socs3", "Socs4", "Socs5", "Socs6", "Socs7", "Sod1",
"Sorbs1", "Sphk1", "Sphk2", "Sptlc1", "Sptlc2", "Sptlc3", "Sptssa", "Sptssb", "Sqle", "Srd5a1", "Srd5a2", "Srd5a3", "Srebf1", "Srebf2",
"St3gal1", "St3gal2", "St3gal3", "St3gal4", "St6galnac1", "St6galnac3", "St6galnac4", "St6galnac5", "St6galnac6", "St8sia2", "St8sia3",
"St8sia4", "St8sia5", "St8sia6", "Star", "Stard3", "Stard4", "Stk11", "Tafazzin", "Tamm41", "Tbxas1", "Tcf7l2", "Tecr", "Tecrl", "Thnsl2",
"Thrsp", "Tlcd3b", "Tm7sf2", "Tm9sf2", "Tmem150a", "Tmem38b", "Tnf", "Trex1", "Trib3", "Tspo", "Ttc7", "Ttc7b", "Ugcg", "Ugt8a", "Uvrag",
"Vac14", "Vapa", "Wdtc1", "Wnt4", "Zbtb20")
lipid_transport <-c("1700057G04Rik", "Abca1", "Abca12", "Abca13", "Abca14", "Abca15", "Abca16", "Abca17", "Abca2", "Abca3", "Abca4", "Abca5",
"Abca6", "Abca7", "Abca8a", "Abca8b", "Abca9", "Abcb11", "Abcb1a", "Abcb1b", "Abcb4", "Abcc1", "Abcc10", "Abcc2", "Abcc3", "Abcc4", "Abcd1",
"Abcd2", "Abcd3", "Abcd4", "Abcg1", "Abcg2", "Abcg4", "Abcg5", "Abcg8", "Acat2", "Ace", "Acsl1", "Acsl3", "Acsl4", "Acsl5", "Acsl6", "Adipoq",
"Agt", "Agtr1a", "Agtr2", "Akt1", "Akt2", "Ano3", "Ano4", "Ano6", "Ano7", "Ano9", "Anxa1", "Anxa2", "Apoa1", "Apoa2", "Apoa4", "Apoa5", "Apob",
"Apobr", "Apoc1", "Apoc2", "Apoc2l", "Apoc3", "Apoc4", "Apod", "Apoe", "Apof", "Apoh", "Apom", "Aqp8", "Aqp9", "Arl8b", "Arv1", "Atg2a",
"Atg2b", "Atg9a", "Atg9b", "Atp10a", "Atp10b", "Atp10d", "Atp11a", "Atp11b", "Atp11c", "Atp5j", "Atp8a1", "Atp8a2", "Atp8b1", "Atp8b2",
"Atp8b3", "Atp8b4", "Atp8b5", "Atp9a", "Atp9b", "Avpr1b", "Bdkrb2", "Bmp6", "C1qtnf1", "C2cd2l", "Cav1", "Cd36", "Ceacam1", "Ceacam2", "Cert1",
"Ces1a", "Ces1b", "Ces1c", "Ces1d", "Ces1e", "Ces1f", "Ces1g", "Cftr", "Cidec", "Cln3", "Commd1", "Cpt1b", "Cptp", "Crabp1", "Crabp2", "Crh",
"Crhr1", "Crot", "Cry1", "Cry2", "Cyp19a1", "Cyp2j5", "Cyp8b1", "Dab2", "Dbi", "Dennd5b", "Dgat1", "Drd2", "Drd3", "Drd4", "Ecrg4", "Edn1",
"Eepd1", "Egf", "Enpp7", "Eprs", "Erfe", "Esyt1", "Esyt2", "Esyt3", "Fabp1", "Fabp12", "Fabp2", "Fabp3", "Fabp4", "Fabp5", "Fabp6", "Fabp7",
"Fabp9", "Fasl", "Fis1", "Furin", "Fzd4", "Gal", "Galr1", "Gdf9", "Ghrl", "Gltp", "Gltpd2", "Gm2a", "Gm37389", "Gm5724", "Gm6614", "Got2",
"Gpihbp1", "Gps2", "Gramd1a", "Gramd1b", "Gramd1c", "Gulp1", "Hbp1", "Hdlbp", "Hnf1a", "Hrh2", "Igfbp3", "Il1a", "Il1b", "Inhba", "Irak1",
"Irs2", "Itgav", "Itgb3", "Kcnn4", "Kcnq1", "Kdm5b", "Kiss1r", "Lamtor1", "Lbp", "Lcat", "Ldlr", "Ldlrap1", "Lep", "Lhcgr", "Lima1", "Lipc",
"Lipg", "Lpcat3", "Lrat", "Lrp1", "Lrp10", "Lrp6", "Map2k6", "Mapk9", "Mexis", "Mfn2", "Mfsd2a", "Mfsd2b", "Mif", "Mip", "Msr1", "Mttp", "Naxe",
"Nfkbia", "Nkx3-1", "Nmb", "Nme4", "Nmur2", "Nos2", "Npc1", "Npc1l1", "Npc2", "Nr1h2", "Nr1h3", "Nr1h4", "Nrg1", "Ntsr1", "Nucb2", "Nus1",
"Oc90", "Osbp", "Osbp2", "Osbpl10", "Osbpl11", "Osbpl1a", "Osbpl2", "Osbpl3", "Osbpl5", "Osbpl6", "Osbpl8", "Osbpl9", "Oxt", "P2rx7", "P2ry2",
"Pcsk9", "Pctp", "Pdzd8", "Pip4k2a", "Pitpna", "Pitpnb", "Pitpnc1", "Pitpnm1", "Pla2g10", "Pla2g12a", "Pla2g12b", "Pla2g1b", "Pla2g2c",
"Pla2g2d", "Pla2g2e", "Pla2g2f", "Pla2g3", "Pla2g4a", "Pla2g4f", "Pla2g5", "Pla2g6", "Pla2r1", "Plekha3", "Plekha8", "Plin2", "Plppr4",
"Plscr1", "Plscr2", "Plscr3", "Plscr4", "Plscr5", "Pltp", "Pmp2", "Pnlip", "Pnpla8", "Pomc", "Pon1", "Pparg", "Prap1", "Prelid1", "Prelid2",
"Prelid3a", "Prelid3b", "Prkcd", "Proca1", "Psap", "Ptch1", "Ptges", "Ptgs2", "Ptpn11", "Rbp1", "Rbp2", "Rbp4", "Rbp7", "Relch", "Ren1",
"Repin1", "Retn", "Rft1", "Rps6kb1", "Runx1", "Sar1b", "Scarb1", "Scarb2", "Scp2", "Scp2d1", "Sec24a", "Selenom", "Serac1", "Sgpp1", "Shh",
"Sigmar1", "Sirt1", "Slc10a1", "Slc10a2", "Slc10a3", "Slc10a4", "Slc10a5", "Slc10a6", "Slc22a22", "Slc25a17", "Slc25a20", "Slc27a1", "Slc27a2",
"Slc27a3", "Slc27a4", "Slc27a5", "Slc27a6", "Slc2a1", "Slc4a1", "Slc51a", "Slc51b", "Slc5a8", "Slc66a2", "Slco1a1", "Slco1a4", "Slco1a5",
"Slco1a6", "Slco1b2", "Slco1c1", "Slco2a1", "Slco2b1", "Slco3a1", "Snord60", "Soat1", "Soat2", "Spg11", "Spns1", "Spns2", "Spns3", "Spp1",
"Spx", "Srebf2", "Sstr4", "Star", "Stard10", "Stard3", "Stard4", "Stard5", "Stard6", "Stoml1", "Stra6", "Stra6l", "Stx12", "Surf4", "Syk",
"Syt7", "Tac1", "Tex2", "Thbs1", "Tmem30a", "Tmem30b", "Tmem30c", "Tmem41b", "Tmf1", "Tnfaip8l3", "Tnfrsf11a", "Tnfsf11", "Tpcn2", "Trem2",
"Triap1", "Trpc5", "Tsku", "Tspo", "Tspo2", "Ttc39b", "Ttc39d", "Ttpa", "Ugcg", "Vamp7", "Vapa", "Vldlr", "Vmp1", "Vps4a", "Vps4b", "Vps51",
"Washc1", "Xkr4", "Xkr5", "Xkr6", "Xkr7", "Xkr8", "Xkr9", "Xrcc4", "Yjefn3", "Zdhhc8")
lipid_sets <- list("lipid_biosynth"=lipid_biosynth,"lipid_transport"=lipid_transport)
gsets <- lipid_sets
# mitch pathways of interest
yy <- mitch_import(x, DEtype="deseq2", geneTable=gt)## Note: Mean no. genes in input = 17755## Note: no. genes in output = 14877## Note: estimated proportion of input genes in output = 0.838res <- mitch_calc(yy, gsets, priority="significance")## Note: When prioritising by significance (ie: small
## p-values), large effect sizes might be missed.head(res$enrichment_result,20)## set setSize pMANOVA s.young s.old p.young
## 1 lipid_biosynth 508 0.0003049783 -0.06187615 -0.09977790 0.01759777
## 2 lipid_transport 277 0.2952926473 0.01995203 -0.01372534 0.56885805
## p.old s.dist SD p.adjustMANOVA
## 1 0.0001288145 0.11740651 0.02680058 0.0006099566
## 2 0.6951110466 0.02421711 0.02381349 0.2952926473unlink("Mst1TG_young_and_old_lipidpathway_mitch.html")
# top N gene heatmap
mitch_report(res, outfile = "Mst1TG_young_and_old_lipidpathway_mitch.html")## Dataset saved as " /tmp/Rtmp0VANOs/Mst1TG_young_and_old_lipidpathway_mitch.rds ".##
##
## processing file: mitch.Rmd##
|
| | 0%
|
|.. | 3%
## inline R code fragments
##
##
|
|.... | 6%
## label: checklibraries (with options)
## List of 1
## $ echo: logi FALSE
##
##
|
|...... | 9%
## ordinary text without R code
##
##
|
|........ | 12%
## label: peek (with options)
## List of 1
## $ echo: logi FALSE
##
##
|
|.......... | 15%
## ordinary text without R code
##
##
|
|............ | 18%
## label: metrics (with options)
## List of 1
## $ echo: logi FALSE
##
##
|
|.............. | 21%
## ordinary text without R code
##
##
|
|................ | 24%
## label: scatterplot (with options)
## List of 5
## $ echo : logi FALSE
## $ fig.height: num 6
## $ fig.width : num 6.5
## $ message : logi FALSE
## $ warning : logi FALSE##
|
|................... | 26%
## ordinary text without R code
##
##
|
|..................... | 29%
## label: contourplot (with options)
## List of 5
## $ echo : logi FALSE
## $ fig.height: num 6
## $ fig.width : num 6.5
## $ warning : logi FALSE
## $ message : logi FALSE##
|
|....................... | 32%
## ordinary text without R code
##
##
|
|......................... | 35%
## label: input_geneset_metrics1 (with options)
## List of 2
## $ results: chr "asis"
## $ echo : logi FALSE
##
##
|
|........................... | 38%
## ordinary text without R code
##
##
|
|............................. | 41%
## label: input_geneset_metrics2 (with options)
## List of 5
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"##
|
|............................... | 44%
## ordinary text without R code
##
##
|
|................................. | 47%
## label: input_geneset_metrics3 (with options)
## List of 5
## $ results : chr "asis"
## $ echo : logi FALSE
## $ message : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7##
|
|................................... | 50%
## ordinary text without R code
##
##
|
|..................................... | 53%
## label: echart1d (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE
##
##
|
|....................................... | 56%
## label: echart2d (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE
##
##
|
|......................................... | 59%
## ordinary text without R code
##
##
|
|........................................... | 62%
## label: heatmap (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 10
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE
##
##
|
|............................................. | 65%
## ordinary text without R code
##
##
|
|............................................... | 68%
## label: effectsize (with options)
## List of 6
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 7
## $ fig.width : num 7
## $ fig.show : chr "all"
## $ message : logi FALSE
##
##
|
|................................................. | 71%
## ordinary text without R code
##
##
|
|................................................... | 74%
## label: results_table (with options)
## List of 2
## $ results: chr "asis"
## $ echo : logi FALSE
##
##
|
|...................................................... | 76%
## ordinary text without R code
##
##
|
|........................................................ | 79%
## label: results_table_complete (with options)
## List of 2
## $ results: chr "asis"
## $ echo : logi FALSE
##
##
|
|.......................................................... | 82%
## ordinary text without R code
##
##
|
|............................................................ | 85%
## label: detailed_geneset_reports1d (with options)
## List of 7
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 6
## $ fig.width : num 6
## $ out.width : chr "80%"
## $ comment : logi NA
## $ message : logi FALSE
##
##
|
|.............................................................. | 88%
## ordinary text without R code
##
##
|
|................................................................ | 91%
## label: detailed_geneset_reports2d (with options)
## List of 7
## $ results : chr "asis"
## $ echo : logi FALSE
## $ fig.height: num 5
## $ fig.width : num 6
## $ out.width : chr "80%"
## $ comment : logi NA
## $ message : logi FALSE##
|
|.................................................................. | 94%
## ordinary text without R code
##
##
|
|.................................................................... | 97%
## label: session_info (with options)
## List of 3
## $ include: logi TRUE
## $ echo : logi TRUE
## $ results: chr "markup"
##
##
|
|......................................................................| 100%
## ordinary text without R code## output file: /mnt/bfx6/bfx/du_xiao/young_mst1tg/integrate/mitch.knit.md## /home/mdz/anaconda3/bin/pandoc +RTS -K512m -RTS /mnt/bfx6/bfx/du_xiao/young_mst1tg/integrate/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmp0VANOs/mitch_report.html --lua-filter /usr/lib/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/lib/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --standalone --section-divs --template /usr/lib/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header /tmp/Rtmp0VANOs/rmarkdown-str22933fb5c6e5.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'##
## Output created: /tmp/Rtmp0VANOs/mitch_report.html## [1] TRUE# heatmaps of pathways of interest
# colour scheme
colfunc <- colorRampPalette(c("blue", "white", "red"))
topsets <- head(res$enrichment_result,50)$set
mytopsets <- gsets[which(names( gsets ) %in% topsets)]
yo <- young[,7:ncol(young)]
colnames(yo) <- paste("y",colnames(yo))
ol <- old[,7:ncol(old)]
colnames(ol) <- paste("o",colnames(ol))
mx <- merge(yo,ol,by=0)
rownames(mx) <- mx$Row.names
mx$Row.names = NULL
i = 1
par(mar = c(10, 8, 8, 4) + 0.2)
for ( i in seq_along(mytopsets) ) {
g <- as.vector(unlist(mytopsets[i]))
symbol <- sapply((strsplit(rownames(mx)," ")),"[[",2)
z <- mx[which(symbol %in% g),]
SETNAME=names(mytopsets[i])
heatmap.2( as.matrix(z), col=colfunc(25),scale="row",
trace="none",margins = c(6,20), cexRow=.4, cexCol=.8)
mtext(SETNAME)
}
System information
sessionInfo()## R version 4.1.2 (2021-11-01)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 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] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] pkgload_1.2.1 GGally_2.1.2 beeswarm_0.4.0 gtools_3.9.2
## [5] echarts4r_0.4.1 mitch_1.4.0 gplots_3.1.1 reshape2_1.4.4
## [9] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7 purrr_0.3.4
## [13] readr_2.0.0 tidyr_1.1.3 tibble_3.1.3 ggplot2_3.3.5
## [17] tidyverse_1.3.1
##
## loaded via a namespace (and not attached):
## [1] bitops_1.0-7 fs_1.5.0 lubridate_1.7.10 RColorBrewer_1.1-2
## [5] httr_1.4.2 rprojroot_2.0.2 tools_4.1.2 backports_1.2.1
## [9] bslib_0.2.5.1 utf8_1.2.2 R6_2.5.0 KernSmooth_2.23-20
## [13] DBI_1.1.1 colorspace_2.0-2 withr_2.4.2 tidyselect_1.1.1
## [17] gridExtra_2.3 compiler_4.1.2 cli_3.0.1 rvest_1.0.0
## [21] xml2_1.3.2 desc_1.3.0 labeling_0.4.2 sass_0.4.0
## [25] caTools_1.18.2 scales_1.1.1 digest_0.6.27 rmarkdown_2.9
## [29] pkgconfig_2.0.3 htmltools_0.5.1.1 dbplyr_2.1.1 fastmap_1.1.0
## [33] highr_0.9 htmlwidgets_1.5.3 rlang_0.4.11 readxl_1.3.1
## [37] rstudioapi_0.13 shiny_1.6.0 jquerylib_0.1.4 generics_0.1.0
## [41] farver_2.1.0 jsonlite_1.7.2 magrittr_2.0.1 Rcpp_1.0.7
## [45] munsell_0.5.0 fansi_0.5.0 lifecycle_1.0.0 stringi_1.7.3
## [49] yaml_2.2.1 MASS_7.3-55 plyr_1.8.6 grid_4.1.2
## [53] parallel_4.1.2 promises_1.2.0.1 crayon_1.4.1 haven_2.4.1
## [57] hms_1.1.0 knitr_1.33 pillar_1.6.1 reprex_2.0.0
## [61] glue_1.4.2 evaluate_0.14 modelr_0.1.8 vctrs_0.3.8
## [65] tzdb_0.1.2 httpuv_1.6.1 cellranger_1.1.0 gtable_0.3.0
## [69] reshape_0.8.8 assertthat_0.2.1 xfun_0.24 mime_0.11
## [73] xtable_1.8-4 broom_0.7.8 later_1.2.0 ellipsis_0.3.2