Reproduce the analysis and regenerate the manuscript
Mark Ziemann & Kaumadi Wijesooriya
2021-12-07
Source: https://github.com/markziemann/SurveyEnrichmentMethods
Intro
This script is designed to enable the complete analysis described in the article to be replicated with a single command.
By knitting this Rmd, it will reanalyse the data and regenerate all figures of the manuscript.
First of all, it is a good idea to check whether all of the requisite dependancies are installed.
Ubuntu users may need to install librsvg2-dev and libv8-dev to get DiagrammeR to work.
# for figure 2 and 3
library("wordcloud")
library("vioplot")
library("reutils")
library("XML")
library("kableExtra")
library("anytime")
# for figure 4
library("getDEE2")
library("DESeq2")
library("clusterProfiler")
library("mitch")
library("kableExtra")
library("eulerr")
library("kableExtra")
library("beeswarm")
# for figure 1 / manuscript draft
library(rmdformats)
library(tidyverse)
library(DiagrammeR)
library(DiagrammeRsvg)
library(rsvg)Execute the scripts
Here will re-run all of the analysis and re-build the manuscript draft.
# Figure 2
rmarkdown::render("analysis_code/analysis1.Rmd")##
##
## processing file: analysis1.Rmd##
|
| | 0%
|
|.. | 3%
## inline R code fragments
##
##
|
|.... | 6%
## label: begin
##
|
|...... | 8%
## ordinary text without R code
##
##
|
|........ | 11%
## label: exclude1
##
|
|.......... | 14%
## ordinary text without R code
##
##
|
|............ | 17%
## label: Journal1##
|
|.............. | 19%
## ordinary text without R code
##
##
|
|................ | 22%
## label: omics1##
|
|.................. | 25%
## ordinary text without R code
##
##
|
|................... | 28%
## label: org1##
|
|..................... | 31%
## ordinary text without R code
##
##
|
|....................... | 33%
## label: gsl1##
|
|......................... | 36%
## ordinary text without R code
##
##
|
|........................... | 39%
## label: gsv1##
|
|............................. | 42%
## ordinary text without R code
##
##
|
|............................... | 44%
## label: test1##
|
|................................. | 47%
## ordinary text without R code
##
##
|
|................................... | 50%
## label: fdr1##
|
|..................................... | 53%
## ordinary text without R code
##
##
|
|....................................... | 56%
## label: app1##
|
|......................................... | 58%
## ordinary text without R code
##
##
|
|........................................... | 61%
## label: appv1##
|
|............................................. | 64%
## ordinary text without R code
##
##
|
|............................................... | 67%
## label: code1##
|
|................................................. | 69%
## ordinary text without R code
##
##
|
|................................................... | 72%
## label: background1##
|
|.................................................... | 75%
## ordinary text without R code
##
##
|
|...................................................... | 78%
## label: genelists1##
|
|........................................................ | 81%
## ordinary text without R code
##
##
|
|.......................................................... | 83%
## label: assumptions1##
|
|............................................................ | 86%
## ordinary text without R code
##
##
|
|.............................................................. | 89%
## label: combined##
|
|................................................................ | 92%
## ordinary text without R code
##
##
|
|.................................................................. | 94%
## label: gseaparam##
|
|.................................................................... | 97%
## ordinary text without R code
##
##
|
|......................................................................| 100%
## label: session## output file: analysis1.knit.md## /usr/bin/pandoc +RTS -K512m -RTS analysis1.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output analysis1.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header /tmp/Rtmp4AKZEm/rmarkdown-str1fbb6a235a566.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'##
## Output created: analysis1.html# Figure 3
rmarkdown::render("analysis_code/analysis2.Rmd")##
##
## processing file: analysis2.Rmd##
|
| | 0%
|
|.... | 5%
## inline R code fragments
##
##
|
|....... | 10%
## label: begin
##
|
|.......... | 15%
## ordinary text without R code
##
##
|
|.............. | 20%
## label: exclude1
##
|
|.................. | 25%
## ordinary text without R code
##
##
|
|..................... | 30%
## label: score##
|
|........................ | 35%
## ordinary text without R code
##
##
|
|............................ | 40%
## label: journal rank
##
|
|................................ | 45%
## ordinary text without R code
##
##
|
|................................... | 50%
## label: scoresvsjrank1##
|
|...................................... | 55%
## ordinary text without R code
##
##
|
|.......................................... | 60%
## label: goodbadugly (with options)
## List of 2
## $ fig.height: num 5
## $ fig.width : num 6##
|
|.............................................. | 65%
## ordinary text without R code
##
##
|
|................................................. | 70%
## label: scoresvsjrank2 (with options)
## List of 2
## $ fig.height: num 5
## $ fig.width : num 6##
|
|.................................................... | 75%
## ordinary text without R code
##
##
|
|........................................................ | 80%
## label: cites
##
|
|............................................................ | 85%
## ordinary text without R code
##
##
|
|............................................................... | 90%
## label: citesplot##
|
|.................................................................. | 95%
## ordinary text without R code
##
##
|
|......................................................................| 100%
## label: session## output file: analysis2.knit.md## /usr/bin/pandoc +RTS -K512m -RTS analysis2.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output analysis2.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header /tmp/Rtmp4AKZEm/rmarkdown-str1fbb6a69b12fac.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'##
## Output created: analysis2.html# uncomment the below line in order to update the number of accumulated
# citations for each article considered
#rmarkdown::render("analysis_code/citation_fetching.Rmd")
# Figure 4
rmarkdown::render("examples/examples.Rmd")##
##
## processing file: examples.Rmd##
|
| | 0%
|
|..... | 7%
## inline R code fragments
##
##
|
|.......... | 14%
## label: begin0
##
|
|............... | 21%
## ordinary text without R code
##
##
|
|.................... | 29%
## label: execute0##
|
|......................... | 36%
## ordinary text without R code
##
##
|
|.............................. | 43%
## label: getdata0 (with options)
## List of 2
## $ fig.width : num 7
## $ fig.height: num 5
##
##
|
|................................... | 50%
## ordinary text without R code
##
##
|
|........................................ | 57%
## label: summary_stats0
##
|
|............................................. | 64%
## ordinary text without R code
##
##
|
|.................................................. | 71%
## label: jacbox0##
|
|....................................................... | 79%
## ordinary text without R code
##
##
|
|............................................................ | 86%
## label: jacbar0##
|
|................................................................. | 93%
## ordinary text without R code
##
##
|
|......................................................................| 100%
## label: session0## output file: examples.knit.md## /usr/bin/pandoc +RTS -K512m -RTS examples.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output examples.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header /tmp/Rtmp4AKZEm/rmarkdown-str1fbb6a10380d79.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --variable code_folding=hide --variable code_menu=1##
## Output created: examples.html# Figure 1 and assemble a manuscript draft
rmarkdown::render("docs/manuscript.Rmd")##
##
## processing file: manuscript.Rmd##
|
| | 0%
|
|....................... | 33%
## inline R code fragments
##
##
|
|............................................... | 67%
## label: diagram1 (with options)
## List of 3
## $ echo : logi FALSE
## $ fig.width : num 8
## $ fig.height: num 4
##
##
|
|......................................................................| 100%
## ordinary text without R code## output file: manuscript.knit.md## Warning: MathJax doesn't work with self_contained when not using the rmarkdown
## "default" template.## /usr/bin/pandoc +RTS -K512m -RTS manuscript.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output manuscript.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --variable 'robobook:true' --variable 'gallery:false' --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 2 --template /usr/local/lib/R/site-library/rmdformats/templates/template.html --highlight-style kate --variable theme=bootstrap --include-in-header /tmp/Rtmp4AKZEm/rmarkdown-str1fbb6a44ad59fa.html##
## Output created: manuscript.html