Mercurial > repos > mingchen0919 > rmarkdown_fastqc_site
changeset 7:d820be692d74 draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
| author | mingchen0919 |
|---|---|
| date | Tue, 08 Aug 2017 12:36:13 -0400 |
| parents | 2f4df2be0572 |
| children | a12e19571cf5 |
| files | 01_evaluation_overview.Rmd 02_fastqc_original_reports.Rmd 1_per_base_quality_scores.Rmd 2_per_base_N_content.Rmd 3_per_sequence_quality_scores.Rmd 4_per_sequence_GC_content.Rmd 5_per_base_sequence_content.Rmd _site.yml fastqc_site.xml fastqc_site_render.R index.Rmd wgcna_construct_network.Rmd wgcna_construct_network.xml wgcna_construct_network_render.R wgcna_eigengene_visualization.Rmd wgcna_eigengene_visualization.xml wgcna_eigengene_visualization_render.R wgcna_preprocessing.Rmd wgcna_preprocessing.xml wgcna_preprocessing_render.R |
| diffstat | 20 files changed, 764 insertions(+), 999 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/01_evaluation_overview.Rmd Tue Aug 08 12:36:13 2017 -0400 @@ -0,0 +1,123 @@ +--- +title: "Evaluation Overview" +output: html_document +--- + +```{r setup, include=FALSE, warning=FALSE, message=FALSE} +knitr::opts_chunk$set(echo = ECHO) +``` + +```{bash 'copy data from datasets directory to working directory', echo=FALSE} +# Copy uploaded data to the working directory +for f in $(echo READS | sed "s/,/ /g") +do + cp $f ./ +done +``` + +```{bash 'run fastqc', echo=FALSE} +# run fastqc and place outputs into the report directory +for r in $(ls *.dat) +do + fastqc -o REPORT_OUTPUT_DIR $r > /dev/null 2>&1 +done +``` + +```{bash 'parse fastqc results', echo=FALSE} +##==== copy fastqc generated zip files from report output directory to job work directory == +cp -r REPORT_OUTPUT_DIR/*zip ./ + +# create a file to store data file paths +echo "sample_id,file_path" > PWF_file_paths.txt # Pass, Warning, Fail +echo "sample_id,file_path" > PBQS_file_paths.txt # Per Base Quality Score +echo "sample_id,file_path" > PSQS_file_paths.txt # Per Sequence Quality Score +echo "sample_id,file_path" > PSGC_file_paths.txt # Per Sequence GC Content +echo "sample_id,file_path" > PBSC_file_paths.txt # Per Base Sequence Content +echo "sample_id,file_path" > PBNC_file_paths.txt # Per Base N Content +echo "sample_id,file_path" > SDL_file_paths.txt # Sequence Duplication Level +echo "sample_id,file_path" > SLD_file_paths.txt # Sequence Length Distribution +echo "sample_id,file_path" > KMC_file_paths.txt # Kmer Content + +for i in $(ls *.zip) +do + BASE=$(echo $i | sed 's/\(.*\)\.zip/\1/g') + echo $BASE + unzip ${BASE}.zip > /dev/null 2>&1 + + ##====== pass,warning,fail (WSF) ============= + awk '/^>>/ {print}' "$BASE"/fastqc_data.txt | grep -v 'END_MODULE' | sed 's/>>//' > "$BASE"-PWF.txt + echo "${BASE},${BASE}-PWF.txt" >> PWF_file_paths.txt + + ##====== per base quality scores (PBQS) ====== + awk '/^>>Per base sequence quality/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-PBQS.txt + echo "${BASE},${BASE}-PBQS.txt" >> PBQS_file_paths.txt + + ##====== per sequence quality scores (PSQS) + awk '/^>>Per sequence quality scores/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-PSQS.txt + echo "${BASE},${BASE}-PSQS.txt" >> PSQS_file_paths.txt + + ##====== Per sequence GC content (PSGC) + awk '/^>>Per sequence GC content/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-PSGC.txt + echo "${BASE},${BASE}-PSGC.txt" >> PSGC_file_paths.txt + + ##====== Per Base Sequence Content (PBSC) + awk '/^>>Per base sequence content/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-PBSC.txt + echo "${BASE},${BASE}-PBSC.txt" >> PBSC_file_paths.txt + + ##====== Per Base N Content (PBNC) + awk '/^>>Per base N content/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-PBNC.txt + echo "${BASE},${BASE}-PBNC.txt" >> PBNC_file_paths.txt + + ##====== Sequence Duplication Level (SDL) + awk '/^>>Sequence Duplication Levels/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-SDL.txt + echo "${BASE},${BASE}-SDL.txt" >> SDL_file_paths.txt + + ##====== Sequence Length Distribution (SLD) + awk '/^>>Sequence Length Distribution/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-SLD.txt + echo "${BASE},${BASE}-SLD.txt" >> SLD_file_paths.txt + + ##====== Kmer Content ============ + awk '/^>>Kmer Content/ {flag=1; next} /END_MODULE/ {flag=0} flag' "$BASE"/fastqc_data.txt >"$BASE"-KMC.txt + echo "${BASE},${BASE}-KMC.txt" >> KMC_file_paths.txt + +done +``` + + +## Evaluation Overview + +```{r 'overview'} +PWF_file_paths = read.csv('PWF_file_paths.txt', + header = TRUE, stringsAsFactors = FALSE) +rm('PWF_df') +for(i in 1:nrow(PWF_file_paths)) { + file_path = PWF_file_paths[i,2] + pwf_df = read.csv(file_path, + sep='\t', header=FALSE, stringsAsFactors = FALSE) + colnames(pwf_df) = c('item', PWF_file_paths[i,1]) + if (!exists('PWF_df')) { + PWF_df = pwf_df + } else { + PWF_df = cbind(PWF_df, pwf_df[,2,drop=FALSE]) + } +} +``` + + +```{r} +my_icon = c('ok', 'remove', 'star') +names(my_icon) = c('pass', 'fail', 'warn') +evaluate_list = list() +for (i in colnames(PWF_df)[-1]) { + evaluate_list[[i]] = formatter( + "span", + style = x ~ style("background-color" = ifelse(x =='pass', '#9CD027', ifelse(x == 'fail', '#CC0000', '#FF4E00')), + "color" = "white", + "width" = "50px", + "float" = "left", + "padding-right" = "5px") + ) +} + +formattable(PWF_df, evaluate_list) +``` \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/02_fastqc_original_reports.Rmd Tue Aug 08 12:36:13 2017 -0400 @@ -0,0 +1,20 @@ +--- +title: "FastQC original reports" +output: html_document +--- + +```{r 'FastQC original reports', include=FALSE, warning=FALSE, message=FALSE} +knitr::opts_chunk$set(echo = ECHO) +``` + + +Below are links to ***Fastqc*** original html reports. + +```{r 'html report links'} +html_report_list = list() +html_files = list.files('REPORT_OUTPUT_DIR', pattern = '.*html') +for (i in html_files) { + html_report_list[[i]] = tags$li(tags$a(href=i, i)) +} +tags$ul(html_report_list) +``` \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/1_per_base_quality_scores.Rmd Tue Aug 08 12:36:13 2017 -0400 @@ -0,0 +1,62 @@ +--- +title: "Per Base Quality Scores" +output: html_document +--- + +```{r setup, include=FALSE, warning=FALSE, message=FALSE} +knitr::opts_chunk$set(echo = ECHO) +``` + + +## Per Base Quality Scores + +```{r} +PBQS_df = data.frame() +PBQS_file_paths = read.csv('PBQS_file_paths.txt', + header = TRUE, stringsAsFactors = FALSE) +for(i in 1:nrow(PBQS_file_paths)) { + # file_path = paste0('REPORT_OUTPUT_DIR/', PBQS_file_paths[i,2]) + file_path = PBQS_file_paths[i,2] + pbqs_df = read.csv(file_path, + sep='\t', header=TRUE, stringsAsFactors = FALSE) %>% + mutate(Base1=as.numeric(str_split_fixed(X.Base, '-', 2)[,1]), + Base2=as.numeric(str_split_fixed(X.Base, '-', 2)[,2])) %>% + (function (df) { + df1 = select(df, -Base2) + df2 = select(df, -Base1) %>% filter(Base2 != '') + colnames(df1) = c(colnames(df1)[1:7], 'Base') + colnames(df2) = c(colnames(df2)[1:7], 'Base') + res = rbind(df1, df2) %>% arrange(Base) + return(res) + }) + pbqs_df$sample_id = rep(PBQS_file_paths[i,1], nrow(pbqs_df)) + PBQS_df = rbind(PBQS_df, pbqs_df) +} +``` + + +```{r} +# datatable(PBQS_df) +max_phred = max(PBQS_df$Mean) + 10 +hchart(PBQS_df, "line", hcaes(x = Base, y = Mean, group = sample_id)) %>% + hc_title( + text = "Per Base Quality Score" + ) %>% + hc_yAxis( + title = list(text = "Mean Base Quality Score"), + min = 0, + max = max_phred, + plotLines = list( + list(label = list(text = "Phred Score = 27"), + width = 2, + dashStyle = "dash", + color = "green", + value = 27), + list(label = list(text = "Phred Score = 20"), + width = 2, + color = "red", + value = 20) + ) + ) %>% + hc_exporting(enabled = TRUE) +```
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/2_per_base_N_content.Rmd Tue Aug 08 12:36:13 2017 -0400 @@ -0,0 +1,58 @@ +--- +title: "Per Base N Content" +output: html_document +--- + +```{r setup, include=FALSE, warning=FALSE, message=FALSE} +knitr::opts_chunk$set(echo = ECHO) +``` + +## Per Base N Content + +```{r} +PBNC_df = data.frame() +PBNC_file_paths = read.csv('PBNC_file_paths.txt', + header = TRUE, stringsAsFactors = FALSE) +for(i in 1:nrow(PBNC_file_paths)) { + # file_path = paste0('REPORT_OUTPUT_DIR/', PBNC_file_paths[i,2]) + file_path = PBNC_file_paths[i,2] + pbnc_df = read.csv(file_path, + sep='\t', header=TRUE, stringsAsFactors = FALSE) %>% + mutate(Base1=as.numeric(str_split_fixed(X.Base, '-', 2)[,1]), + Base2=as.numeric(str_split_fixed(X.Base, '-', 2)[,2])) %>% + (function (df) { + df1 = select(df, -Base2) + df2 = select(df, -Base1) %>% filter(Base2 != '') + colnames(df1) = c(colnames(df1)[1:2], 'Base') + colnames(df2) = c(colnames(df2)[1:2], 'Base') + res = rbind(df1, df2) %>% arrange(Base) + return(res) + }) + pbnc_df$sample_id = rep(PBNC_file_paths[i,1], nrow(pbnc_df)) + PBNC_df = rbind(PBNC_df, pbnc_df) +} +``` + + +```{r} +PBNC_df$N.Count = PBNC_df$N.Count * 100 +max_phred = max(PBNC_df$N.Count) + 5 +hchart(PBNC_df, "line", hcaes(x = as.character(Base), y = N.Count, group = sample_id)) %>% + hc_title( + text = "Per Base N Content" + ) %>% + hc_xAxis( + title = list(text = "Base Position") + ) %>% + hc_yAxis( + title = list(text = "N %"), + plotLines = list( + list(label = list(text = "N = 5%"), + width = 2, + dashStyle = "dash", + color = "red", + value = 5) + ) + ) %>% + hc_exporting(enabled = TRUE) +```
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/3_per_sequence_quality_scores.Rmd Tue Aug 08 12:36:13 2017 -0400 @@ -0,0 +1,50 @@ +--- +title: "Per Sequence Quality Scores" +output: html_document +--- + +```{r setup, include=FALSE, warning=FALSE, message=FALSE} +knitr::opts_chunk$set(echo = ECHO) +``` + +## Per Sequence Quality Scores + +```{r} +PSQS_df = data.frame() +PSQS_file_paths = read.csv('PSQS_file_paths.txt', + header = TRUE, stringsAsFactors = FALSE) +for(i in 1:nrow(PSQS_file_paths)) { + # file_path = paste0('REPORT_OUTPUT_DIR/', PSQS_file_paths[i,2]) + file_path = PSQS_file_paths[i,2] + psqs_df = read.csv(file_path, + sep='\t', header=TRUE, stringsAsFactors = FALSE) + psqs_df$sample_id = rep(PSQS_file_paths[i,1], nrow(psqs_df)) + PSQS_df = rbind(PSQS_df, psqs_df) +} +``` + + +```{r} +max_phred = max(PSQS_df$X.Quality) + 5 +hchart(PSQS_df, "line", hcaes(x = X.Quality, y = Count, group = sample_id)) %>% + hc_title( + text = "Per Sequence Quality Score" + ) %>% + hc_xAxis( + title = list(text = "Mean Sequence Quality Score"), + min = 0, + max = max_phred, + plotLines = list( + list(label = list(text = "Phred Score = 27"), + width = 2, + dashStyle = "dash", + color = "green", + value = 27), + list(label = list(text = "Phred Score = 20"), + width = 2, + color = "red", + value = 20) + ) + ) %>% + hc_exporting(enabled = TRUE) +```
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/4_per_sequence_GC_content.Rmd Tue Aug 08 12:36:13 2017 -0400 @@ -0,0 +1,38 @@ +--- +title: "Per Sequence GC Content" +output: html_document +--- + +```{r setup, include=FALSE, warning=FALSE, message=FALSE} +knitr::opts_chunk$set(echo = ECHO) +``` + +## Per Sequence GC Content + + +```{r} +PSGC_df = data.frame() +PSGC_file_paths = read.csv('PSGC_file_paths.txt', + header = TRUE, stringsAsFactors = FALSE) +for(i in 1:nrow(PSGC_file_paths)) { + # file_path = paste0('REPORT_OUTPUT_DIR/', PSGC_file_paths[i,2]) + file_path = PSGC_file_paths[i,2] + psgc_df = read.csv(file_path, + sep='\t', header=TRUE, stringsAsFactors = FALSE) + psgc_df$sample_id = rep(PSGC_file_paths[i,1], nrow(psgc_df)) + PSGC_df = rbind(PSGC_df, psgc_df) +} +``` + + +```{r} +max_phred = max(PSGC_df$Count) + 5 +hchart(PSGC_df, "line", hcaes(x = X.GC.Content, y = Count, group = sample_id)) %>% + hc_title( + text = "Per Sequence GC Content" + ) %>% + hc_xAxis( + title = list(text = "% GC") + ) %>% + hc_exporting(enabled = TRUE) +```
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/5_per_base_sequence_content.Rmd Tue Aug 08 12:36:13 2017 -0400 @@ -0,0 +1,45 @@ +--- +title: "Per Base Sequence Content" +output: html_document +--- + +```{r setup, include=FALSE, warning=FALSE, message=FALSE} +knitr::opts_chunk$set(echo = ECHO) +``` + +## Per Base Sequence Content + +```{r} +PBSC_df = data.frame() +PBSC_file_paths = read.csv('PBSC_file_paths.txt', + header = TRUE, stringsAsFactors = FALSE) +for(i in 1:nrow(PBSC_file_paths)) { + # file_path = paste0('REPORT_OUTPUT_DIR/', PBSC_file_paths[i,2]) + file_path = PBSC_file_paths[i,2] + pbsc_df = read.csv(file_path, + sep='\t', header=TRUE, stringsAsFactors = FALSE) %>% + mutate(Base1=as.numeric(str_split_fixed(X.Base, '-', 2)[,1]), + Base2=as.numeric(str_split_fixed(X.Base, '-', 2)[,2])) %>% + (function (df) { + df1 = select(df, -Base2) + df2 = select(df, -Base1) %>% filter(Base2 != '') + colnames(df1) = c(colnames(df1)[1:5], 'Base') + colnames(df2) = c(colnames(df2)[1:5], 'Base') + res = rbind(df1, df2) %>% arrange(Base) + return(res) + }) + pbsc_df$sample_id = rep(PBSC_file_paths[i,1], nrow(pbsc_df)) + PBSC_df = rbind(PBSC_df, pbsc_df) +} +``` + + +```{r out.width="100%"} +PBSC_df_2 = select(PBSC_df, -X.Base) %>% + melt(id = c('Base', 'sample_id'), value.name = 'base_percentage') +p = ggplot(data = PBSC_df_2, aes(x = Base, y = base_percentage, group = variable, color = variable)) + + geom_line() + + facet_wrap(~ sample_id) +ggplotly(p) +``` +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/_site.yml Tue Aug 08 12:36:13 2017 -0400 @@ -0,0 +1,29 @@ +name: "FastQC Website" +output_dir: "my_site" +navbar: + title: "FastQC" + type: inverse + left: + - text: "Home" + icon: fa-home + href: index.html + - text: "Evaluation Overview" + href: 01_evaluation_overview.html + - text: "Evaluation Items" + menu: + - text: "Per Base Quality Scores" + href: 1_per_base_quality_scores.html + - text: "Per Base N Content" + href: 2_per_base_N_content.html + - text: "Per Sequence Quality Scores" + href: 3_per_sequence_quality_scores.html + - text: "Per Sequence GC Content" + href: 4_per_sequence_GC_content.html + - text: "Per Base Sequence Content" + href: 5_per_base_sequence_content.html + - text: "Original FastQC Reports" + href: 02_fastqc_original_reports.html +output: + html_document: + theme: cosmo + highlight: textmate \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastqc_site.xml Tue Aug 08 12:36:13 2017 -0400 @@ -0,0 +1,124 @@ +<tool id="fastqc_site" name="Fastqc Site" version="1.0.0"> + <requirements> + <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement> + <requirement type="package" version="1.20.0">r-getopt</requirement> + <requirement type="package" version="1.2">r-rmarkdown</requirement> + <requirement type="package" version="1.8.4">r-plyr</requirement> + <requirement type="package" version="1.1.0">r-stringr</requirement> + <requirement type="package" version="0.5.0">r-highcharter</requirement> + <requirement type="package" version="0.2">r-dt</requirement> + <requirement type="package" version="1.4.2">r-reshape2</requirement> + <requirement type="package" version="4.5.6">r-plotly</requirement> + <requirement type="package" version="0.2.0.1">r-formattable</requirement> + <requirement type="package" version="0.3.5">r-htmltools</requirement> + <requirement type="package" version="0.11.5">fastqc</requirement> + </requirements> + <description> + Implements FastQC analysis and display results in R Markdown website. + </description> + <stdio> + <regex match="Execution halted" + source="both" + level="fatal" + description="Execution halted." /> + <regex match="Error in" + source="both" + level="fatal" + description="An undefined error occured, please check your intput carefully and contact your administrator." /> + <regex match="Fatal error" + source="both" + level="fatal" + description="An undefined error occured, please check your intput carefully and contact your administrator." /> + </stdio> + <command> + <![CDATA[ + + Rscript '${__tool_directory__}/fastqc_site_render.R' + + ## 1. input data + -r $reads + -e $echo + + ## 2. output report and report site directory + -o $fastqc_site + -d $fastqc_site.files_path + + ## 3. Rmd templates sitting in the tool directory + + ## _site.yml and index.Rmd template files + -s '${__tool_directory__}/_site.yml' + -i '${__tool_directory__}/index.Rmd' + + ## other Rmd body template files + -p '${__tool_directory__}/01_evaluation_overview.Rmd' + -a '${__tool_directory__}/02_fastqc_original_reports.Rmd' + -b '${__tool_directory__}/1_per_base_quality_scores.Rmd' + -c '${__tool_directory__}/2_per_base_N_content.Rmd' + -f '${__tool_directory__}/3_per_sequence_quality_scores.Rmd' + -g '${__tool_directory__}/4_per_sequence_GC_content.Rmd' + -h '${__tool_directory__}/5_per_base_sequence_content.Rmd' + + ]]> + </command> + <inputs> + <param format="fastq,fastq.gz,fastq.bz2,bam,sam" multiple="true" name="reads" type="data" label="Short reads data from history" /> + <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" /> + </inputs> + <outputs> + <data format="html" name="fastqc_site" label="fastqc site" /> + </outputs> + <citations> + <citation type="bibtex"> + @misc{bioinformatics2014fastqc, + title={FastQC}, + author={Bioinformatics, Babraham}, + year={2014} + } + </citation> + <citation type="bibtex"> + @article{allaire2016rmarkdown, + title={rmarkdown: Dynamic Documents for R, 2016}, + author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob}, + journal={R package version 0.9}, + volume={6}, + year={2016} + } + </citation> + <citation type="bibtex"> + @book{xie2015dynamic, + title={Dynamic Documents with R and knitr}, + author={Xie, Yihui}, + volume={29}, + year={2015}, + publisher={CRC Press} + } + </citation> + <citation type="bibtex"> + @misc{plotly2017, + title = {plotly: Create Interactive Web Graphics via 'plotly.js'}, + author = {Carson Sievert and Chris Parmer and Toby Hocking and Scott Chamberlain and Karthik Ram and Marianne Corvellec and Pedro Despouy}, + year = {2017}, + note = {R package version 4.6.0}, + url = {https://CRAN.R-project.org/package=plotly}, + } + </citation> + <citation type="bibtex"> + @misc{highcharter2017, + title = {highcharter: A Wrapper for the 'Highcharts' Library}, + author = {Joshua Kunst}, + year = {2017}, + note = {R package version 0.5.0}, + url = {https://CRAN.R-project.org/package=highcharter}, + } + </citation> + <citation type="bibtex"> + @misc{formattable2016, + title = {formattable: Create 'Formattable' Data Structures}, + author = {Kun Ren and Kenton Russell}, + year = {2016}, + note = {R package version 0.2.0.1}, + url = {https://CRAN.R-project.org/package=formattable}, + } + </citation> + </citations> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastqc_site_render.R Tue Aug 08 12:36:13 2017 -0400 @@ -0,0 +1,195 @@ +##======= Handle arguments from command line ======== +# setup R error handline to go to stderr +options(show.error.messages=FALSE, + error=function(){ + cat(geterrmessage(), file=stderr()) + quit("no", 1, F) + }) + +# we need that to not crash galaxy with an UTF8 error on German LC settings. +loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +# suppress warning +options(warn = -1) + +options(stringsAsFactors=FALSE, useFancyQuotes=FALSE) +args = commandArgs(trailingOnly=TRUE) + +suppressPackageStartupMessages({ + library(getopt) + library(tools) +}) + +# column 1: the long flag name +# column 2: the short flag alias. A SINGLE character string +# column 3: argument mask +# 0: no argument +# 1: argument required +# 2: argument is optional +# column 4: date type to which the flag's argument shall be cast. +# possible values: logical, integer, double, complex, character. +spec_list=list() + +##------- 1. input data --------------------- +spec_list$READS = c('reads', 'r', '1', 'character') +spec_list$ECHO = c('echo', 'e', '1', 'character') + +##--------2. output report and report site directory -------------- +spec_list$FASTQC_SITE = c('fastqc_site', 'o', '1', 'character') +spec_list$FASTQC_SITE_DIR = c('fastqc_site_dir', 'd', '1', 'character') + +##--------3. Rmd templates sitting in the tool directory ---------- + + ## _site.yml and index.Rmd files + spec_list$SITE_YML = c('site_yml', 's', 1, 'character') + spec_list$INDEX_Rmd = c('index_rmd', 'i', 1, 'character') + + ## other Rmd body template files + spec_list$x01 = c('x01_evaluation_overview', 'p', '1', 'character') + spec_list$x02 = c('x02_fastqc_original_reports', 'a', '1', 'character') + spec_list$x1 = c('x1_per_base_quality_scores', 'b', '1', 'character') + spec_list$x2 = c('x2_per_base_N_content', 'c', '1', 'character') + spec_list$x3 = c('x3_per_sequence_quality_scores', 'f', '1', 'character') + spec_list$x4 = c('x4_per_sequence_GC_content', 'g', '1', 'character') + spec_list$x5 = c('x5_per_base_sequence_content', 'h', '1', 'character') + +##------------------------------------------------------------------ + +spec = t(as.data.frame(spec_list)) +opt = getopt(spec) +# arguments are accessed by long flag name (the first column in the spec matrix) +# NOT by element name in the spec_list +# example: opt$help, opt$expression_file +##====== End of arguments handling ========== + +#------ Load libraries --------- +library(rmarkdown) +library(plyr) +library(stringr) +library(dplyr) +library(highcharter) +library(DT) +library(reshape2) +library(plotly) +library(formattable) +library(htmltools) + + +#----- 1. create the report directory ------------------------ +paste0('mkdir -p ', opt$fastqc_site_dir) %>% + system() + +#----- 2. generate Rmd files with Rmd templates -------------- +# a. templates without placeholder variables: +# copy templates from tool directory to the working directory. +# b. templates with placeholder variables: +# substitute variables with user input values and place them in the working directory. + + + #----- Copy index.Rmd and _site.yml files to job working direcotry ----- + file.copy(opt$index_rmd, 'index.Rmd', recursive=TRUE) + file.copy(opt$site_yml, '_site.yml', recursive=TRUE) + #--------------------------------------------------------- + + #----- 01_evaluation_overview.Rmd ----------------------- + readLines(opt$x01_evaluation_overview) %>% + (function(x) { + gsub('ECHO', opt$echo, x) + }) %>% + (function(x) { + gsub('READS', opt$reads, x) + }) %>% + (function(x) { + gsub('REPORT_OUTPUT_DIR', opt$fastqc_site_dir, x) + }) %>% + (function(x) { + fileConn = file('01_evaluation_overview.Rmd') + writeLines(x, con=fileConn) + close(fileConn) + }) + + #----- 1_per_base_quality_scores.Rmd -------------------- + readLines(opt$x1_per_base_quality_scores) %>% + (function(x) { + gsub('ECHO', opt$echo, x) + }) %>% + (function(x) { + fileConn = file('1_per_base_quality_scores.Rmd') + writeLines(x, con=fileConn) + close(fileConn) + }) + + #----- 2_per_base_N_content.Rmd ------------------------- + readLines(opt$x2_per_base_N_content) %>% + (function(x) { + gsub('ECHO', opt$echo, x) + }) %>% + (function(x) { + fileConn = file('2_per_base_N_content.Rmd') + writeLines(x, con=fileConn) + close(fileConn) + }) + + #----- 3_per_sequence_quality_scores.Rmd ---------------- + readLines(opt$x3_per_sequence_quality_scores) %>% + (function(x) { + gsub('ECHO', opt$echo, x) + }) %>% + (function(x) { + fileConn = file('3_per_sequence_quality_scores.Rmd') + writeLines(x, con=fileConn) + close(fileConn) + }) + + + #----- 4_per_sequence_GC_content.Rmd -------------------- + readLines(opt$x4_per_sequence_GC_content) %>% + (function(x) { + gsub('ECHO', opt$echo, x) + }) %>% + (function(x) { + fileConn = file('4_per_sequence_GC_content.Rmd') + writeLines(x, con=fileConn) + close(fileConn) + }) + + + #----- 5_per_base_sequence_content.Rmd ------------------ + readLines(opt$x5_per_base_sequence_content) %>% + (function(x) { + gsub('ECHO', opt$echo, x) + }) %>% + (function(x) { + fileConn = file('5_per_base_sequence_content.Rmd') + writeLines(x, con=fileConn) + close(fileConn) + }) + + #----- 02_fastqc_original_reports.Rmd ------------------- + readLines(opt$x02_fastqc_original_reports) %>% + (function(x) { + gsub('ECHO', opt$echo, x) + }) %>% + (function(x) { + gsub('REPORT_OUTPUT_DIR', opt$fastqc_site_dir, x) + }) %>% + (function(x) { + fileConn = file('02_fastqc_original_reports.Rmd') + writeLines(x, con=fileConn) + close(fileConn) + }) + + + +#------ 3. render all Rmd files with render_site() -------- +render_site() + + +#-------4. manipulate outputs ----------------------------- +# a. copy index.html to the report output path +# b. copy all files in 'my_site' to the report output directory +file.copy('my_site/index.html', opt$fastqc_site, recursive=TRUE) +paste0('cp -r my_site/* ', opt$fastqc_site_dir) %>% + system() + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/index.Rmd Tue Aug 08 12:36:13 2017 -0400 @@ -0,0 +1,20 @@ +--- +title: "FastQC Report" +output: html_document +--- + +```{r setup, include=FALSE, warning=FALSE, message=FALSE} +knitr::opts_chunk$set(echo = TRUE) +``` + + + +## References + +* Andrews, Simon. "FastQC: a quality control tool for high throughput sequence data." (2010): 175-176. +* Goecks, Jeremy, Anton Nekrutenko, and James Taylor. "Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences." Genome biology 11.8 (2010): R86. +* Afgan, Enis, et al. "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update." Nucleic acids research (2016): gkw343. +* Highcharts. https://www.highcharts.com/. (access by May 26, 2017). +* R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/. +* Joshua Kunst (2017). highcharter: A Wrapper for the 'Highcharts' Library. R package version 0.5.0. https://CRAN.R-project.org/package=highcharter +* Carson Sievert, Chris Parmer, Toby Hocking, Scott Chamberlain, Karthik Ram, Marianne Corvellec and Pedro Despouy (2017). plotly: Create Interactive Web Graphics via 'plotly.js'. R package version 4.6.0. https://CRAN.R-project.org/package=plotly
--- a/wgcna_construct_network.Rmd Tue Aug 08 12:35:11 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,178 +0,0 @@ ---- -title: 'WGCNA: construct network' -output: - html_document: - number_sections: true - toc: true - theme: cosmo - highlight: tango ---- - -```{r setup, include=FALSE, warning=FALSE, message=FALSE} -knitr::opts_chunk$set( - echo = ECHO -) -``` - -# Import workspace - -This step imports workspace from the **WGCNA: preprocessing** step. - -```{r} -fcp = file.copy("PREPROCESSING_WORKSPACE", "deseq.RData") -load("deseq.RData") -``` - - -# Processing outliers {.tabset} - -## Before removing outliers - -```{r} -plot(sampleTree, main = "Sample clustering to detect outliers", sub="", xlab="", cex.lab = 1.5, - cex.axis = 1, cex.main = 1, cex = 0.5) -if(!is.na(HEIGHT_CUT)) { - # plot a line to show the cut - abline(h = HEIGHT_CUT, col = "red") - # determine cluster under the line - clust = cutreeStatic(sampleTree, cutHeight = HEIGHT_CUT, minSize = 10) - keepSamples = (clust==1) - expression_data = expression_data[keepSamples, ] -} -``` - -## After removing outliers - -```{r} -sampleTree = hclust(dist(expression_data), method = "average"); -plot(sampleTree, main = "Sample clustering to detect outliers", sub="", xlab="", - cex.axis = 1, cex.main = 1, cex = 0.5) -``` - - -# Trait data {.tabeset} - -If trait data is provided, the first 100 rows from the data will be displayed here. A plot consisting of sample cluster dendrogram and trait heatmap will also be gerenated. - -## Trait data table - -```{r} -trait_data = data.frame() -if ("TRAIT_DATA" != 'None') { - trait_data = read.csv("TRAIT_DATA", header = TRUE, row.names = 1) - # form a data frame analogous to expression data that will hold the traits. - sample_names = rownames(expression_data) - trait_rows = match(sample_names, rownames(trait_data)) - trait_data = trait_data[trait_rows, ] - datatable(head(trait_data, 100), style="bootstrap", filter = 'top', - class="table-condensed", options = list(dom = 'tp', scrollX = TRUE)) -} -``` - -## Dendrogram and heatmap - -```{r fig.align='center', fig.width=8, fig.height=9} -if (nrow(trait_data) != 0) { - traitColors = numbers2colors(trait_data, signed = FALSE) - plotDendroAndColors(sampleTree, traitColors, - groupLabels = names(trait_data), - main = "Sample dendrogram and trait heatmap", - cex.dendroLabels = 0.5) -} -``` - - -# The thresholding power - -```{r} -powers = c(1:10, seq(12, 20, 2)) -soft_threshold = pickSoftThreshold(expression_data, powerVector = powers, verbose = 5) -``` - -```{r fig.align='center'} -par(mfrow=c(1,2)) -plot(soft_threshold$fitIndices[,1], -sign(soft_threshold$fitIndices[,3])*soft_threshold$fitIndices[,2], - xlab="Soft Threshold (power)", - ylab="Scale Free Topology Model Fit,signed R^2",type="n", - main = paste("Scale independence"), - cex.lab = 0.5); -text(soft_threshold$fitIndices[,1], -sign(soft_threshold$fitIndices[,3])*soft_threshold$fitIndices[,2], - labels=powers,cex=0.5,col="red"); - -# calculate soft threshold power -y = -sign(soft_threshold$fitIndices[,3])*soft_threshold$fitIndices[,2] -r2_cutoff = 0.9 -for(i in 1:length(powers)) { - if(y[i] > r2_cutoff) { - soft_threshold_power = soft_threshold$fitIndices[,1][i] - r2_cutoff_new = y[i] - break - } - soft_threshold_power = soft_threshold$fitIndices[,1][length(powers)] -} -abline(h=r2_cutoff, col="red") -abline(v=soft_threshold_power, col="blue") -text(soft_threshold_power+1, r2_cutoff-0.1, - paste0('R^2 cutoff = ', round(r2_cutoff_new,2)), - cex = 0.5, col = "red") - -plot(soft_threshold$fitIndices[,1], soft_threshold$fitIndices[,5], - xlab="Soft Threshold (power)",ylab="Mean Connectivity", type="n", - main = paste("Mean connectivity"), - cex.lab = 0.5) -text(soft_threshold$fitIndices[,1], soft_threshold$fitIndices[,5], labels=powers, cex=0.5,col="red") -par(mfrow=c(1,1)) -``` - - -# Construct network - -The gene network is constructed based on **soft threshold power = `r soft_threshold_power`** - -```{r} -gene_network = blockwiseModules(expression_data, power = soft_threshold_power, - TOMType = "unsigned", minModuleSize = 30, - reassignThreshold = 0, mergeCutHeight = 0.25, - numericLabels = TRUE, pamRespectsDendro = FALSE, - verbose = 3) -``` - - -# Gene modules {.tabset} - -## Idenfity gene modules - -```{r} -modules = table(gene_network$colors) -n_modules = length(modules) - 1 -module_size_upper = modules[2] -module_size_lower = modules[length(modules)] - -module_table = data.frame(model_label = c(0, 1:n_modules), - gene_size = as.vector(modules)) -datatable(t(module_table)) -``` - -The results above indicates that there are **`r n_modules` gene modules**, labeled 1 through `r length(n_modules)` in order of descending size. The largest module has **`r module_size_upper` genes**, and the smallest module has **`r module_size_lower` genes**. The label 0 is reserved for genes outside of all modules. - - -## Dendrogram and module plot - -```{r} -# Convert labels to colors for plotting -module_colors = labels2colors(gene_network$colors) -# Plot the dendrogram and the module colors underneath -plotDendroAndColors(gene_network$dendrograms[[1]], module_colors[gene_network$blockGenes[[1]]], - "Module colors", - dendroLabels = FALSE, hang = 0.03, - addGuide = TRUE, guideHang = 0.05) -``` - - -```{r echo=FALSE} -# save workspace -rm("opt") -save(list=ls(all.names = TRUE), file='CONSTRUCT_NETWORK_WORKSPACE') -``` - -
--- a/wgcna_construct_network.xml Tue Aug 08 12:35:11 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,105 +0,0 @@ -<tool id="wgcna_construct_network" name="WGCNA: construct network" version="1.0.0"> - <requirements> - <requirement type="package" version="1.20.0">r-getopt</requirement> - <requirement type="package" version="1.2">r-rmarkdown</requirement> - <requirement type="package" version="1.8.4">r-plyr</requirement> - <requirement type="package" version="0.4.0">r-highcharter</requirement> - <requirement type="package" version="0.2">r-dt</requirement> - <requirement type="package" version="0.3.5">r-htmltools</requirement> - <requirement type="package" version="1.51">r-wgcna</requirement> - </requirements> - <description> - Construct gene network. - </description> - <stdio> - <regex match="Execution halted" - source="both" - level="fatal" - description="Execution halted." /> - <regex match="Error in" - source="both" - level="fatal" - description="An undefined error occured, please check your intput carefully and contact your administrator." /> - <regex match="Fatal error" - source="both" - level="fatal" - description="An undefined error occured, please check your intput carefully and contact your administrator." /> - </stdio> - <command> - <![CDATA[ - - Rscript '${__tool_directory__}/wgcna_construct_network_render.R' - - ## 1. input data - -e $echo - -w $preprocessing_workspace - -h '$height_cut' - -t $trait_data - - - - ## 2. output report and report site directory - -o $wgcna_construct_network - -d $wgcna_construct_network.files_path - -W $construct_network_workspace - - - ## 3. Rmd templates in the tool directory - - ## _site.yml and index.Rmd template files - -M '${__tool_directory__}/wgcna_construct_network.Rmd' - - - - ]]> - </command> - <inputs> - <param type="data" name="preprocessing_workspace" format="rdata" optional="false" - label="R workspace from WGCNA: preprocessing" /> - <param type="float" name="height_cut" optional="true" label="Height" - help="Refer to the sample clustering plot from WGCNA: preprocessing and choose a height cut that will - remove outliers. If there is not outlier, leave this field blank." /> - <param type="data" name="trait_data" format="csv" optional="true" - label="Trait data" - help="If trait data is provided, a plot consisting of sample clustering and trait heatmap will - be generated. This field is optional. "/> - - <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" /> - </inputs> - <outputs> - <data name="wgcna_construct_network" format="html" label="WGCNA: construct_network" /> - <data name="construct_network_workspace" format="rdata" label="R workspace: WGCNA construct_network" /> - </outputs> - <citations> - <citation type="bibtex"> - @article{langfelder2008wgcna, - title={WGCNA: an R package for weighted correlation network analysis}, - author={Langfelder, Peter and Horvath, Steve}, - journal={BMC bioinformatics}, - volume={9}, - number={1}, - pages={559}, - year={2008}, - publisher={BioMed Central} - } - </citation> - <citation type="bibtex"> - @article{allaire2016rmarkdown, - title={rmarkdown: Dynamic Documents for R, 2016}, - author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob}, - journal={R package version 0.9}, - volume={6}, - year={2016} - } - </citation> - <citation type="bibtex"> - @book{xie2015dynamic, - title={Dynamic Documents with R and knitr}, - author={Xie, Yihui}, - volume={29}, - year={2015}, - publisher={CRC Press} - } - </citation> - </citations> -</tool> \ No newline at end of file
--- a/wgcna_construct_network_render.R Tue Aug 08 12:35:11 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,112 +0,0 @@ -##======= Handle arguments from command line ======== -# setup R error handline to go to stderr -options(show.error.messages=FALSE, - error=function(){ - cat(geterrmessage(), file=stderr()) - quit("no", 1, F) - }) - -# we need that to not crash galaxy with an UTF8 error on German LC settings. -loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") - -# suppress warning -options(warn = -1) - -options(stringsAsFactors=FALSE, useFancyQuotes=FALSE) -args = commandArgs(trailingOnly=TRUE) - -suppressPackageStartupMessages({ - library(getopt) - library(tools) -}) - -# column 1: the long flag name -# column 2: the short flag alias. A SINGLE character string -# column 3: argument mask -# 0: no argument -# 1: argument required -# 2: argument is optional -# column 4: date type to which the flag's argument shall be cast. -# possible values: logical, integer, double, complex, character. -spec_list=list() - -##------- 1. input data --------------------- -spec_list$ECHO = c('echo', 'e', '1', 'character') -spec_list$PREPROCESSING_WORKSPACE = c('preprocessing_workspace', 'w', '1', 'character') -spec_list$HEIGHT_CUT = c('height_cut', 'h', '2', 'double') -spec_list$TRAIT_DATA = c('trait_data', 't', '2', 'character') - - -##--------2. output report and report site directory -------------- -spec_list$OUTPUT_HTML = c('wgcna_construct_network_html', 'o', '1', 'character') -spec_list$OUTPUT_DIR = c('wgcna_construct_network_dir', 'd', '1', 'character') -spec_list$CONSTRUCT_NETWORK_WORKSPACE = c('construct_network_workspace', 'W', '1', 'character') - - -##--------3. Rmd templates in the tool directory ---------- - -spec_list$WGCNA_PREPROCESSING_RMD = c('wgcna_construct_network_rmd', 'M', '1', 'character') - - - -##------------------------------------------------------------------ - -spec = t(as.data.frame(spec_list)) -opt = getopt(spec) -# arguments are accessed by long flag name (the first column in the spec matrix) -# NOT by element name in the spec_list -# example: opt$help, opt$expression_file -##====== End of arguments handling ========== - -#------ Load libraries --------- -library(rmarkdown) -library(WGCNA) -library(DT) -library(htmltools) -library(ggplot2) - - -#----- 1. create the report directory ------------------------ -system(paste0('mkdir -p ', opt$wgcna_construct_network_dir)) - - -#----- 2. generate Rmd files with Rmd templates -------------- -# a. templates without placeholder variables: -# copy templates from tool directory to the working directory. -# b. templates with placeholder variables: -# substitute variables with user input values and place them in the working directory. - - -#----- 01 wgcna_construct_network.Rmd ----------------------- -readLines(opt$wgcna_construct_network_rmd) %>% - (function(x) { - gsub('ECHO', opt$echo, x) - }) %>% - (function(x) { - gsub('PREPROCESSING_WORKSPACE', opt$preprocessing_workspace, x) - }) %>% - (function(x) { - gsub('HEIGHT_CUT', opt$height_cut, x) - }) %>% - (function(x) { - gsub('TRAIT_DATA', opt$trait_data, x) - }) %>% - (function(x) { - gsub('OUTPUT_DIR', opt$wgcna_construct_network_dir, x) - }) %>% - (function(x) { - gsub('CONSTRUCT_NETWORK_WORKSPACE', opt$construct_network_workspace, x) - }) %>% - (function(x) { - fileConn = file('wgcna_construct_network.Rmd') - writeLines(x, con=fileConn) - close(fileConn) - }) - - -#------ 3. render all Rmd files -------- -render('wgcna_construct_network.Rmd', output_file = opt$wgcna_construct_network_html) - -#-------4. manipulate outputs ----------------------------- - -
--- a/wgcna_eigengene_visualization.Rmd Tue Aug 08 12:35:11 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,121 +0,0 @@ ---- -title: 'WGCNA: eigengene visualization' -output: - html_document: - number_sections: true - toc: true - theme: cosmo - highlight: tango ---- - -```{r setup, include=FALSE, warning=FALSE, message=FALSE} -knitr::opts_chunk$set( - echo = ECHO -) -``` - -# Import workspace - -This step imports workspace from the **WGCNA: construct network** step. - -```{r} -fcp = file.copy("CONSTRUCT_NETWORK_WORKSPACE", "deseq.RData") -load("deseq.RData") -``` - - -# Gene modules {.tabset} - -```{r} -if(!is.na(SOFT_THRESHOLD_POWER)) soft_threshold_power = SOFT_THRESHOLD_POWER -``` - -## Identify gene modules - -The gene network is constructed based on **soft threshold power = `r soft_threshold_power`** - -```{r} -gene_network = blockwiseModules(expression_data, power = soft_threshold_power, - TOMType = "unsigned", minModuleSize = 30, - reassignThreshold = 0, mergeCutHeight = 0.25, - numericLabels = TRUE, pamRespectsDendro = FALSE, - verbose = 3) -``` - - -```{r} -modules = table(gene_network$colors) -n_modules = length(modules) - 1 -module_size_upper = modules[2] -module_size_lower = modules[length(modules)] - -module_table = data.frame(model_label = c(0, 1:n_modules), - gene_size = as.vector(modules)) -datatable(t(module_table)) -``` - -The results above indicates that there are **`r n_modules` gene modules**, labeled 1 through `r length(n_modules)` in order of descending size. The largest module has **`r module_size_upper` genes**, and the smallest module has **`r module_size_lower` genes**. The label 0 is reserved for genes outside of all modules. - - -## Dendrogram and module plot - -```{r} -# Convert labels to colors for plotting -module_colors = labels2colors(gene_network$colors) -# Plot the dendrogram and the module colors underneath -plotDendroAndColors(gene_network$dendrograms[[1]], module_colors[gene_network$blockGenes[[1]]], - "Module colors", - dendroLabels = FALSE, hang = 0.03, - addGuide = TRUE, guideHang = 0.05) -``` - - -# Gene module correlation - -We can calculate eigengenes and use them as representative profiles to quantify similarity of found gene modules. - -```{r} -n_genes = ncol(expression_data) -n_samples = nrow(expression_data) -``` - -```{r} -diss_tom = 1-TOMsimilarityFromExpr(expression_data, power = soft_threshold_power) -set.seed(123) -select_genes = sample(n_genes, size = PLOT_GENES) -select_diss_tom = diss_tom[select_genes, select_genes] - -# calculate gene tree on selected genes -select_gene_tree = hclust(as.dist(select_diss_tom), method = 'average') -select_module_colors = module_colors[select_genes] - -# transform diss_tom with a power to make moderately strong connections more visiable in the heatmap. -plot_diss_tom = select_diss_tom^7 -# set diagonal to NA for a nicer plot -diag(plot_diss_tom) = NA -``` - - -```{r fig.align='center'} -TOMplot(plot_diss_tom, select_gene_tree, select_module_colors, main = "Network heatmap") -``` - - -# Eigengene visualization {.tabset} - -## Eigengene dendrogram - -```{r fig.align='center'} -module_eigengenes = moduleEigengenes(expression_data, module_colors)$eigengenes -plotEigengeneNetworks(module_eigengenes, "Eigengene dendrogram", - plotHeatmaps = FALSE) -``` - -## Eigengene adjacency heatmap - -```{r fig.align='center'} -plotEigengeneNetworks(module_eigengenes, "Eigengene adjacency heatmap", - marHeatmap = c(2, 3, 2, 2), - plotDendrograms = FALSE, xLabelsAngle = 90) -``` -
--- a/wgcna_eigengene_visualization.xml Tue Aug 08 12:35:11 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,100 +0,0 @@ -<tool id="wgcna_eigengene_visualization" name="WGCNA: eigengene visualization" version="1.0.0"> - <requirements> - <requirement type="package" version="1.20.0">r-getopt</requirement> - <requirement type="package" version="1.2">r-rmarkdown</requirement> - <requirement type="package" version="1.8.4">r-plyr</requirement> - <requirement type="package" version="0.4.0">r-highcharter</requirement> - <requirement type="package" version="0.2">r-dt</requirement> - <requirement type="package" version="0.3.5">r-htmltools</requirement> - <requirement type="package" version="1.51">r-wgcna</requirement> - </requirements> - <description> - Eigengene visualization. - </description> - <stdio> - <regex match="Execution halted" - source="both" - level="fatal" - description="Execution halted." /> - <regex match="Error in" - source="both" - level="fatal" - description="An undefined error occured, please check your intput carefully and contact your administrator." /> - <regex match="Fatal error" - source="both" - level="fatal" - description="An undefined error occured, please check your intput carefully and contact your administrator." /> - </stdio> - <command> - <![CDATA[ - ## Add tools to PATH - export PATH=/opt/R-3.2.5/bin:\$PATH && - - Rscript '${__tool_directory__}/wgcna_eigengene_visualization_render.R' - - ## 1. input data - -e $echo - -w $construct_network_workspace - -p '$soft_threshold_power' - -n $plot_genes - - - ## 2. output report and report site directory - -o $wgcna_eigengene_visualization - -d $wgcna_eigengene_visualization.files_path - - ## 3. Rmd templates in the tool directory - - -M '${__tool_directory__}/wgcna_eigengene_visualization.Rmd' - - - - ]]> - </command> - <inputs> - <param type="data" name="construct_network_workspace" format="rdata" optional="false" - label="R workspace from WGCNA: construct network" /> - <param type="integer" name="soft_threshold_power" optional="true" label="Soft threshold power" - help="Refer to the scale independence plot from 'WGCNA: construct network' and choose an optimal soft threshold power. - An optimal power will be calculated automatically if no value is provided." /> - <param type="integer" name="plot_genes" value="400" min="1" label="Number of genes" optional="false" - help="The number of genes that will be used. It is possible to speed up the plotting by providing a subset of - genes. However, the gene dendrogram may ofter look different from dendrogram of all genes." /> - <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" /> - </inputs> - <outputs> - <data name="wgcna_eigengene_visualization" format="html" label="WGCNA: eigengene visualization" /> - </outputs> - <citations> - <citation type="bibtex"> - @article{langfelder2008wgcna, - title={WGCNA: an R package for weighted correlation network analysis}, - author={Langfelder, Peter and Horvath, Steve}, - journal={BMC bioinformatics}, - volume={9}, - number={1}, - pages={559}, - year={2008}, - publisher={BioMed Central} - } - </citation> - <citation type="bibtex"> - @article{allaire2016rmarkdown, - title={rmarkdown: Dynamic Documents for R, 2016}, - author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob}, - journal={R package version 0.9}, - volume={6}, - year={2016} - } - </citation> - <citation type="bibtex"> - @book{xie2015dynamic, - title={Dynamic Documents with R and knitr}, - author={Xie, Yihui}, - volume={29}, - year={2015}, - publisher={CRC Press} - } - </citation> - </citations> -</tool> \ No newline at end of file
--- a/wgcna_eigengene_visualization_render.R Tue Aug 08 12:35:11 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,109 +0,0 @@ -##======= Handle arguments from command line ======== -# setup R error handline to go to stderr -options(show.error.messages=FALSE, - error=function(){ - cat(geterrmessage(), file=stderr()) - quit("no", 1, F) - }) - -# we need that to not crash galaxy with an UTF8 error on German LC settings. -loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") - -# suppress warning -options(warn = -1) - -options(stringsAsFactors=FALSE, useFancyQuotes=FALSE) -args = commandArgs(trailingOnly=TRUE) - -suppressPackageStartupMessages({ - library(getopt) - library(tools) -}) - -# column 1: the long flag name -# column 2: the short flag alias. A SINGLE character string -# column 3: argument mask -# 0: no argument -# 1: argument required -# 2: argument is optional -# column 4: date type to which the flag's argument shall be cast. -# possible values: logical, integer, double, complex, character. -spec_list=list() - -##------- 1. input data --------------------- -spec_list$ECHO = c('echo', 'e', '1', 'character') -spec_list$CONSTRUCT_NETWORK_WORKSPACE = c('construct_network_workspace', 'w', '1', 'character') -spec_list$SOFT_THRESHOLD_POWER = c('soft_threshold_power', 'p', '2', 'double') -spec_list$PLOT_GENES = c('plot_genes', 'n', '1', 'integer') - - -##--------2. output report and report site directory -------------- -spec_list$OUTPUT_HTML = c('wgcna_eigengene_visualization_html', 'o', '1', 'character') -spec_list$OUTPUT_DIR = c('wgcna_eigengene_visualization_dir', 'd', '1', 'character') - - - -##--------3. Rmd templates in the tool directory ---------- - -spec_list$WGCNA_EIGENGENE_VISUALIZATION_RMD = c('wgcna_eigengene_visualization_rmd', 'M', '1', 'character') - - - -##------------------------------------------------------------------ - -spec = t(as.data.frame(spec_list)) -opt = getopt(spec) -# arguments are accessed by long flag name (the first column in the spec matrix) -# NOT by element name in the spec_list -# example: opt$help, opt$expression_file -##====== End of arguments handling ========== - -#------ Load libraries --------- -library(rmarkdown) -library(WGCNA) -library(DT) -library(htmltools) -library(ggplot2) - - -#----- 1. create the report directory ------------------------ -system(paste0('mkdir -p ', opt$wgcna_eigengene_visualization_dir)) - - -#----- 2. generate Rmd files with Rmd templates -------------- -# a. templates without placeholder variables: -# copy templates from tool directory to the working directory. -# b. templates with placeholder variables: -# substitute variables with user input values and place them in the working directory. - - -#----- 01 wgcna_eigengene_visualization.Rmd ----------------------- -readLines(opt$wgcna_eigengene_visualization_rmd) %>% - (function(x) { - gsub('ECHO', opt$echo, x) - }) %>% - (function(x) { - gsub('CONSTRUCT_NETWORK_WORKSPACE', opt$construct_network_workspace, x) - }) %>% - (function(x) { - gsub('SOFT_THRESHOLD_POWER', opt$soft_threshold_power, x) - }) %>% - (function(x) { - gsub('PLOT_GENES', opt$plot_genes, x) - }) %>% - (function(x) { - gsub('OUTPUT_DIR', opt$wgcna_eigengene_visualization_dir, x) - }) %>% - (function(x) { - fileConn = file('wgcna_eigengene_visualization.Rmd') - writeLines(x, con=fileConn) - close(fileConn) - }) - - -#------ 3. render all Rmd files -------- -render('wgcna_eigengene_visualization.Rmd', output_file = opt$wgcna_eigengene_visualization_html) - -#-------4. manipulate outputs ----------------------------- - -
--- a/wgcna_preprocessing.Rmd Tue Aug 08 12:35:11 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,76 +0,0 @@ ---- -title: 'WGCNA: data preprocessing' -output: - html_document: - number_sections: true - toc: true - theme: cosmo - highlight: tango ---- - -```{r setup, include=FALSE, warning=FALSE, message=FALSE} -knitr::opts_chunk$set( - echo = ECHO -) -``` - -```{r} -str(opt) -``` - -# Import data - -Each row represents a gene and each column represents a sample. - -```{r} -expression_data = read.csv('EXPRESSION_DATA', header = TRUE, row.names = 1) -``` - -Display the first 100 genes. - -```{r} -datatable(head(expression_data, 100), style="bootstrap", filter = 'top', - class="table-condensed", options = list(dom = 'tp', scrollX = TRUE)) -``` - -Transpose expression data matrix so that each row represents a sample and each column represents a gene. - -```{r} -expression_data = as.data.frame(t(expression_data)) -``` - -# Checking data - -Checking data for excessive missing values and identification of outlier microarray samples. - -```{r} -gsg = goodSamplesGenes(expression_data, verbose = 3) -if (!gsg$allOK) { - # Optionally, print the gene and sample names that were removed: - if (sum(!gsg$goodGenes)>0) - printFlush(paste("Removing genes:", paste(names(expression_data)[!gsg$goodGenes], collapse = ", "))); - if (sum(!gsg$goodSamples)>0) - printFlush(paste("Removing samples:", paste(rownames(expression_data)[!gsg$goodSamples], collapse = ", "))); - # Remove the offending genes and samples from the data: - expression_data = expression_data[gsg$goodSamples, gsg$goodGenes] -} else { - print('all genes are OK!') -} -``` - -# Clustering samples - -If there are any outliers, choose a height cut that will remove the offending sample. Remember this number since you will need this number in further analysis. - -```{r fig.align='center'} -sampleTree = hclust(dist(expression_data), method = "average"); -plot(sampleTree, main = "Sample clustering to detect outliers", sub="", xlab="", - cex.axis = 1, cex.main = 1, cex = 0.5) -``` - - -```{r echo=FALSE} -rm("opt") -save(list=ls(all.names = TRUE), file='PREPROCESSING_WORKSPACE') -``` -
--- a/wgcna_preprocessing.xml Tue Aug 08 12:35:11 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,96 +0,0 @@ -<tool id="wgcna_preprocessing" name="WGCNA: preprocessing" version="1.0.0"> - <requirements> - <requirement type="package" version="1.20.0">r-getopt</requirement> - <requirement type="package" version="1.2">r-rmarkdown</requirement> - <requirement type="package" version="1.8.4">r-plyr</requirement> - <requirement type="package" version="0.4.0">r-highcharter</requirement> - <requirement type="package" version="0.2">r-dt</requirement> - <requirement type="package" version="0.3.5">r-htmltools</requirement> - <requirement type="package" version="1.51">r-wgcna</requirement> - </requirements> - <description> - Data clearning and preprocessing. - </description> - <stdio> - <regex match="Execution halted" - source="both" - level="fatal" - description="Execution halted." /> - <regex match="Error in" - source="both" - level="fatal" - description="An undefined error occured, please check your intput carefully and contact your administrator." /> - <regex match="Fatal error" - source="both" - level="fatal" - description="An undefined error occured, please check your intput carefully and contact your administrator." /> - </stdio> - <command> - <![CDATA[ - ## Add tools to PATH - export PATH=/opt/R-3.2.5/bin:\$PATH && - - Rscript '${__tool_directory__}/wgcna_preprocessing_render.R' - - ## 1. input data - -e $echo - -E $expression_data - - - ## 2. output report and report site directory - -o $wgcna_preprocessing - -d $wgcna_preprocessing.files_path - -w $preprocessing_workspace - - ## 3. Rmd templates sitting in the tool directory - - ## _site.yml and index.Rmd template files - -D '${__tool_directory__}/wgcna_preprocessing.Rmd' - - - - ]]> - </command> - <inputs> - <param type="data" name="expression_data" format="csv" optional="false" label="Gene expression data" - help="Each row represents a gene and each column represents a sample."/> - - <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" /> - </inputs> - <outputs> - <data name="wgcna_preprocessing" format="html" label="WGCNA: preprocessing" /> - <data name="preprocessing_workspace" format="rdata" label="R workspace: WGCNA preprocessing" /> - </outputs> - <citations> - <citation type="bibtex"> - @article{langfelder2008wgcna, - title={WGCNA: an R package for weighted correlation network analysis}, - author={Langfelder, Peter and Horvath, Steve}, - journal={BMC bioinformatics}, - volume={9}, - number={1}, - pages={559}, - year={2008}, - publisher={BioMed Central} - } - </citation> - <citation type="bibtex"> - @article{allaire2016rmarkdown, - title={rmarkdown: Dynamic Documents for R, 2016}, - author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob}, - journal={R package version 0.9}, - volume={6}, - year={2016} - } - </citation> - <citation type="bibtex"> - @book{xie2015dynamic, - title={Dynamic Documents with R and knitr}, - author={Xie, Yihui}, - volume={29}, - year={2015}, - publisher={CRC Press} - } - </citation> - </citations> -</tool> \ No newline at end of file
--- a/wgcna_preprocessing_render.R Tue Aug 08 12:35:11 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,102 +0,0 @@ -##======= Handle arguments from command line ======== -# setup R error handline to go to stderr -options(show.error.messages=FALSE, - error=function(){ - cat(geterrmessage(), file=stderr()) - quit("no", 1, F) - }) - -# we need that to not crash galaxy with an UTF8 error on German LC settings. -loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") - -# suppress warning -options(warn = -1) - -options(stringsAsFactors=FALSE, useFancyQuotes=FALSE) -args = commandArgs(trailingOnly=TRUE) - -suppressPackageStartupMessages({ - library(getopt) - library(tools) -}) - -# column 1: the long flag name -# column 2: the short flag alias. A SINGLE character string -# column 3: argument mask -# 0: no argument -# 1: argument required -# 2: argument is optional -# column 4: date type to which the flag's argument shall be cast. -# possible values: logical, integer, double, complex, character. -spec_list=list() - -##------- 1. input data --------------------- -spec_list$ECHO = c('echo', 'e', '1', 'character') -spec_list$EXPRESSION_DATA = c('expression_data', 'E', '1', 'character') - - -##--------2. output report and report site directory -------------- -spec_list$OUTPUT_HTML = c('wgcna_preprocessing_html', 'o', '1', 'character') -spec_list$OUTPUT_DIR = c('wgcna_preprocessing_dir', 'd', '1', 'character') -spec_list$PREPROCESSING_WORKSPACE = c('preprocessing_workspace', 'w', '1', 'character') - -##--------3. Rmd templates sitting in the tool directory ---------- - -spec_list$WGCNA_PREPROCESSING_RMD = c('wgcna_preprocessing_rmd', 'D', '1', 'character') - - - -##------------------------------------------------------------------ - -spec = t(as.data.frame(spec_list)) -opt = getopt(spec) -# arguments are accessed by long flag name (the first column in the spec matrix) -# NOT by element name in the spec_list -# example: opt$help, opt$expression_file -##====== End of arguments handling ========== - -#------ Load libraries --------- -library(rmarkdown) -library(WGCNA) -library(DT) -library(htmltools) - - -#----- 1. create the report directory ------------------------ -system(paste0('mkdir -p ', opt$wgcna_preprocessing_dir)) - - -#----- 2. generate Rmd files with Rmd templates -------------- -# a. templates without placeholder variables: -# copy templates from tool directory to the working directory. -# b. templates with placeholder variables: -# substitute variables with user input values and place them in the working directory. - - -#----- 01 wgcna_preprocessing.Rmd ----------------------- -readLines(opt$wgcna_preprocessing_rmd) %>% - (function(x) { - gsub('ECHO', opt$echo, x) - }) %>% - (function(x) { - gsub('EXPRESSION_DATA', opt$expression_data, x) - }) %>% - (function(x) { - gsub('OUTPUT_DIR', opt$wgcna_preprocessing_dir, x) - }) %>% - (function(x) { - gsub('PREPROCESSING_WORKSPACE', opt$preprocessing_workspace, x) - }) %>% - (function(x) { - fileConn = file('wgcna_preprocessing.Rmd') - writeLines(x, con=fileConn) - close(fileConn) - }) - - -#------ 3. render all Rmd files -------- -render('wgcna_preprocessing.Rmd', output_file = opt$wgcna_preprocessing_html) - -#-------4. manipulate outputs ----------------------------- - -