# HG changeset patch # User vmarcon # Date 1516279477 18000 # Node ID 46ddb0591d8b35631e80b4c301257e70d50c9cc1 planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556 diff -r 000000000000 -r 46ddb0591d8b LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE Thu Jan 18 07:44:37 2018 -0500 @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +the GNU General Public License is intended to guarantee your freedom to +share and change all versions of a program--to make sure it remains free +software for all its users. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + {project} Copyright (C) {year} {fullname} + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff -r 000000000000 -r 46ddb0591d8b static/images/ChangeDatatype.pdf Binary file static/images/ChangeDatatype.pdf has changed diff -r 000000000000 -r 46ddb0591d8b static/images/descriptive_stat_all.png Binary file static/images/descriptive_stat_all.png has changed diff -r 000000000000 -r 46ddb0591d8b static/images/descriptive_stat_boxplot.png Binary file static/images/descriptive_stat_boxplot.png has changed diff -r 000000000000 -r 46ddb0591d8b static/images/descriptive_stat_density.png Binary file static/images/descriptive_stat_density.png has changed diff -r 000000000000 -r 46ddb0591d8b static/images/descriptive_stat_histo.png Binary file static/images/descriptive_stat_histo.png has changed diff -r 000000000000 -r 46ddb0591d8b static/images/descriptive_stat_maplot.png Binary file static/images/descriptive_stat_maplot.png has changed diff -r 000000000000 -r 46ddb0591d8b static/images/descriptive_stat_pairs.png Binary file static/images/descriptive_stat_pairs.png has changed diff -r 000000000000 -r 46ddb0591d8b static/images/input_count_file.png Binary file static/images/input_count_file.png has changed diff -r 000000000000 -r 46ddb0591d8b summary_statistics.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/summary_statistics.R Thu Jan 18 07:44:37 2018 -0500 @@ -0,0 +1,263 @@ +########################################################################### +# Quality controls and descriptive analysis plots # +########################################################################### +# Authors: Melanie Petera # +########################################################################### +# Description : This script allows various displays of data for quality # +# control and descriptive analysis. The input data is a matrix of # +# quantitative variables, and it returns chosen plots in png format # +# and a table with chosen statistics. # +########################################################################### +# Specific R packages: # +# - edgeR (needed for MA plots) # +########################################################################### +# Version 1 (06-06-2014): display boxplot, histogram, density plot, # +# MA plot, pairs plot, and return a table of chosen statistics # +# (quantiles, mean, variance, standard error of the mean) # +########################################################################### + +desc_fct <- function(file.in, nacode, table_file, graph_file, stat, chosen.stat, ploting, chosen.plot, log_file){ + # Parameters: + # - file.in: count matrix input (tab-separated) [file name] + # - nacode: missing value coding character + # - table_file: results file containing table of chosen statistics [file name] + # - graph_file: pdf file containing plots for chosen statistics [file name] + # - stat: should statistics be calculated? (TRUE/FALSE) + # - chosen.stat: character listing the chosen statistics (comma-separated) + # - ploting: should graphics be displayed? (TRUE/FALSE) + # - chosen.plot: character listing the chosen plots (comma-separated) + # - log_file: a log file [file name] + + +########################################################## +# Read and verify data - - - - - - - - - - - - +# Checks valids for all modules + +library(methods) + +log_error=function(message="") { + line_use="line" + column_use="column" + + cat("Normalization report\n",file=log_file,append=F,sep="") + cat("⚠ An error occurred while trying to read your table.\n
",file=log_file,append=T,sep="") + cat("Please check that:\n
",file=log_file,append=T,sep="") + cat("
    \n",file=log_file,append=T,sep="") + cat("
  • the table you want to process contains the same number of columns for each line
    • \n",file=log_file,append=T,sep="") + cat("
  • the first line of your table is a header line (specifying the name of each ",column_use,")
    • \n",file=log_file,append=T,sep="") + cat("
  • the first column of your table specifies the name of each ",line_use,"
    • \n",file=log_file,append=T,sep="") + cat("
  • both individual and variable names should be unique
    • \n",file=log_file,append=T,sep="") + cat("
  • each value is separated from the other by a TAB character
    • \n",file=log_file,append=T,sep="") + cat("
  • except for first line and first column, table should contain a numeric value
    • \n",file=log_file,append=T,sep="") + cat("
  • this value may contain character '.' as decimal separator or '",nacode,"' for missing values
    • \n",file=log_file,append=T,sep="") + cat("
\n",file=log_file,append=T,sep="") + cat("-------
\nError messages recieved:
\n",conditionMessage(message),"\n",file=log_file,append=T,sep="") + cat("\n",file=log_file,append=T,sep="") + q(save="no",status=1) +} + +tab_in=tryCatch( + { + tab_in=read.table(file.in,header=TRUE,na.strings=nacode,sep="\t",check.names=FALSE,quote="\"") + }, + error=function(cond) { + log_error(message=cond) + return(NA) + }, + warning=function(cond) { + log_error(message=cond) + return(NA) + }, + finally={ + #Do nothing special + } +) + +if (ncol(tab_in)<2) { + log_error(simpleCondition("The table you want to use contains less than two columns.")) +} + +rn=as.character(tab_in[,1]) +if (length(rn)!=length(unique(rn))) { + duplicated_rownames=table(rn) + duplicated_rownames=duplicated_rownames[duplicated_rownames>1] + duplicated_rownames=names(duplicated_rownames) + if (length(duplicated_rownames)>3) { + duplicated_rownames=c(duplicated_rownames[1:3],"...") + } + duplicated_rownames=paste(duplicated_rownames,collapse=", ") + log_error(simpleCondition( + paste("The table you want to use have duplicated values in the first column (", + " - duplicated names: ",duplicated_rownames,sep="") + )) +} +tab=tab_in[,-1] +rownames(tab)=rn + +#Check all columns are numerical +tab=as.matrix(tab) +cell.with.na=c() +for (i in 1:ncol(tab)) { + na.v1=is.na(tab[,i]) + na.v2=is.na(as.numeric(tab[,i])) + if (sum(na.v1)!=sum(na.v2)) { + sel=which(na.v1!=na.v2) + sel=sel[1] + value=tab[sel,i] + log_error(simpleCondition( + paste("Column '",colnames(tab)[i],"' of your table contains non numerical values. Please check its content (on line #",sel,": value='",value,"').",sep="") + )) + } + if (length(cell.with.na)==0 & sum(na.v1)!=0) { + cell.with.na=c(i,which(na.v1)[1]) + } +} + +Dataset <- tab_in + +########################################################## +# Statistics table computation - - - - - - - - - + +log="" + +if(stat=="T" & length(chosen.stat)!=0){ + + stat.list <- strsplit(chosen.stat,",")[[1]] + stat.res <- t(Dataset[0,,drop=FALSE]) + + numdig <- 5 + + if("mean" %in% stat.list){ + stat.res <- cbind(stat.res,c("Mean",round(colMeans(Dataset[,-1],na.rm=TRUE),digits=numdig))) + } + + if("sd" %in% stat.list){ + colSd <- apply(Dataset[,-1],2,sd,na.rm=TRUE) + stat.res <- cbind(stat.res,c("Std.Dev",round(colSd,digits=numdig))) + } + + if("variance" %in% stat.list){ + colVar <- apply(Dataset[,-1],2,var,na.rm=TRUE) + stat.res <- cbind(stat.res,c("Variance",round(colVar,digits=numdig))) + } + + if(("median" %in% stat.list)&&(!("quartile" %in% stat.list))){ + colMed <- apply(Dataset[,-1],2,median,na.rm=TRUE) + stat.res <- cbind(stat.res,c("Median",round(colMed,digits=numdig))) + } + + if("quartile" %in% stat.list){ + colQ <- round(apply(Dataset[,-1],2,quantile,na.rm=TRUE),digits=numdig) + stat.res <- cbind(stat.res,c("Min",colQ[1,]),c("Q1",colQ[2,]), + c("Median",colQ[3,]),c("Q3",colQ[4,]),c("Max",colQ[5,])) + } + + if("decile" %in% stat.list){ + colD <- round(t(apply(Dataset[,-1],2,quantile,na.rm=TRUE,seq(0,1,0.1))),digits=numdig) + colD <- rbind(paste("D",seq(0,10,1),sep=""),colD) + stat.res <- cbind(stat.res,colD) + } + + write.table(stat.res,table_file,col.names=FALSE,sep="\t",quote=FALSE) + + log=paste(log,"➔ You choose to compute :",chosen.stat,"
") + +} # end if(stat) +else{ + log=paste(log,"➔ You don't choose any stats
") +} + +########################################################## +# Graphics generation - - - - - - - - - - - - - + +if(ploting=="T" & length(chosen.plot)!=0){ + + nb_graph_per_row=4 + nb_graph=ncol(Dataset)-1 + + nb_row=round(nb_graph/nb_graph_per_row) + + nb_empty_plot=nb_graph %% nb_graph_per_row + if (nb_empty_plot != 0) { + nb_row=nb_row+1 + } + + page_height=3.5 * nb_row + + pdf(file=graph_file,height=page_height) + + graph.list <- strsplit(chosen.plot,",")[[1]] + + #For the pair plot, we stick to the default layout + if("pairsplot" %in% graph.list){ + pairs(Dataset[,-1]) + } + + #For the other plots, we have 4 plots per line + par(mfrow=c(nb_row,nb_graph_per_row),mar=c(3, 3, 3, 1) + 0.1) + + if("boxplot" %in% graph.list){ + for(ech in 2:ncol(Dataset)){ + boxplot(Dataset[,ech],main=colnames(Dataset)[ech],xlab=NULL) + } + #Complete page with empty plots + i=0; while (i") +} # end if(ploting) +else{ + log=paste(log,"➔ You don't choose any plot
") +} + + + +########################################################## +# Treatment successfull +########################################################## +cat("Summary statistics report\n",file=log_file,append=F,sep="") +cat(log,file=log_file,append=T,sep="") +cat("✓ Your process is successfull!
",file=log_file,append=T,sep="") +cat("\n",file=log_file,append=T,sep="") + + +} # end of function + + diff -r 000000000000 -r 46ddb0591d8b summary_statistics.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/summary_statistics.xml Thu Jan 18 07:44:37 2018 -0500 @@ -0,0 +1,280 @@ + + + + Produce simple descriptive statistics from a numerical table + + R + bioconductor-edger + bioconductor-limma + r-batch + r-locfit + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (stat_cond['stat'] == 'T') + + + (ploting_cond['ploting'] == 'T') + + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r 46ddb0591d8b summary_statistics_galaxy.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/summary_statistics_galaxy.R Thu Jan 18 07:44:37 2018 -0500 @@ -0,0 +1,52 @@ +########################################################################### +# Quality controls and descriptive analysis plots # +########################################################################### +# Authors: Melanie Petera # +########################################################################### +# Description : This script allows various displays of data for quality # +# control and descriptive analysis. The input data is a matrix of # +# quantitative variables, and it returns chosen plots in png format # +# and a table with chosen statistics. # +########################################################################### +# Specific R packages: # +# - edgeR (needed for MA plots) # +########################################################################### +# Version 1 (06-06-2014): display boxplot, histogram, density plot, # +# MA plot, pairs plot, and return a table of chosen statistics # +# (quantiles, mean, variance, standard error of the mean) # +########################################################################### + + +##------------------------------ +## Libraries laoding +##------------------------------ +# For parseCommandArgs function +library(batch) + +# R script call +source_local <- function(fname) +{ + argv <- commandArgs(trailingOnly = FALSE) + base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) + source(paste(base_dir, fname, sep="/")) +} + +#Import the different functions used for Summary_Statistics +source_local("summary_statistics.R") + +##------------------------------ +## Lecture parametres +##------------------------------ +argLs <- parseCommandArgs(evaluate=FALSE) + +desc_fct(file.in=argLs[["file_in"]], +nacode=argLs[["NA_code"]], +table_file=argLs[["table_file"]], +graph_file=argLs[["graph_file"]], +stat=argLs[["stat"]], +chosen.stat=argLs[["stat_chosen"]], +ploting=argLs[["ploting"]], +chosen.plot=argLs[["plot_chosen"]], +log_file=argLs[["log_file"]]) + + diff -r 000000000000 -r 46ddb0591d8b test-data/decathlon.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/decathlon.tsv Thu Jan 18 07:44:37 2018 -0500 @@ -0,0 +1,42 @@ +"name" "100m" "Long.jump" "Shot.put" "High.jump" "400m" "110m.hurdle" "Discus" "Pole.vault" "Javeline" "1500m" +"SEBRLE" 11.04 7.58 14.83 2.07 49.81 14.69 43.75 5.02 63.19 291.7 +"CLAY" 10.76 7.4 14.26 1.86 49.37 14.05 50.72 4.92 60.15 301.5 +"KARPOV" 11.02 7.3 14.77 2.04 48.37 14.09 48.95 4.92 50.31 300.2 +"BERNARD" 11.02 7.23 14.25 1.92 48.93 14.99 40.87 5.32 62.77 280.1 +"YURKOV" 11.34 7.09 15.19 2.1 50.42 15.31 46.26 4.72 63.44 276.4 +"WARNERS" 11.11 7.6 14.31 1.98 48.68 14.23 41.1 4.92 51.77 278.1 +"ZSIVOCZKY" 11.13 7.3 13.48 2.01 48.62 14.17 45.67 4.42 55.37 268 +"McMULLEN" 10.83 7.31 13.76 2.13 49.91 14.38 44.41 4.42 56.37 285.1 +"MARTINEAU" 11.64 6.81 14.57 1.95 50.14 14.93 47.6 4.92 52.33 262.1 +"HERNU" 11.37 7.56 14.41 1.86 51.1 15.06 44.99 4.82 57.19 285.1 +"BARRAS" 11.33 6.97 14.09 1.95 49.48 14.48 42.1 4.72 55.4 282 +"NOOL" 11.33 7.27 12.68 1.98 49.2 15.29 37.92 4.62 57.44 266.6 +"BOURGUIGNON" 11.36 6.8 13.46 1.86 51.16 15.67 40.49 5.02 54.68 291.7 +"Sebrle" 10.85 7.84 16.36 2.12 48.36 14.05 48.72 5 70.52 280.01 +"Clay" 10.44 7.96 15.23 2.06 49.19 14.13 50.11 4.9 69.71 282 +"Karpov" 10.5 7.81 15.93 2.09 46.81 13.97 51.65 4.6 55.54 278.11 +"Macey" 10.89 7.47 15.73 2.15 48.97 14.56 48.34 4.4 58.46 265.42 +"Warners" 10.62 7.74 14.48 1.97 47.97 14.01 43.73 4.9 55.39 278.05 +"Zsivoczky" 10.91 7.14 15.31 2.12 49.4 14.95 45.62 4.7 63.45 269.54 +"Hernu" 10.97 7.19 14.65 2.03 48.73 14.25 44.72 4.8 57.76 264.35 +"Nool" 10.8 7.53 14.26 1.88 48.81 14.8 42.05 5.4 61.33 276.33 +"Bernard" 10.69 7.48 14.8 2.12 49.13 14.17 44.75 4.4 55.27 276.31 +"Schwarzl" 10.98 7.49 14.01 1.94 49.76 14.25 42.43 5.1 56.32 273.56 +"Pogorelov" 10.95 7.31 15.1 2.06 50.79 14.21 44.6 5 53.45 287.63 +"Schoenbeck" 10.9 7.3 14.77 1.88 50.3 14.34 44.41 5 60.89 278.82 +"Barras" 11.14 6.99 14.91 1.94 49.41 14.37 44.83 4.6 64.55 267.09 +"Smith" 10.85 6.81 15.24 1.91 49.27 14.01 49.02 4.2 61.52 272.74 +"Averyanov" 10.55 7.34 14.44 1.94 49.72 14.39 39.88 4.8 54.51 271.02 +"Ojaniemi" 10.68 7.5 14.97 1.94 49.12 15.01 40.35 4.6 59.26 275.71 +"Smirnov" 10.89 7.07 13.88 1.94 49.11 14.77 42.47 4.7 60.88 263.31 +"Qi" 11.06 7.34 13.55 1.97 49.65 14.78 45.13 4.5 60.79 272.63 +"Drews" 10.87 7.38 13.07 1.88 48.51 14.01 40.11 5 51.53 274.21 +"Parkhomenko" 11.14 6.61 15.69 2.03 51.04 14.88 41.9 4.8 65.82 277.94 +"Terek" 10.92 6.94 15.15 1.94 49.56 15.12 45.62 5.3 50.62 290.36 +"Gomez" 11.08 7.26 14.57 1.85 48.61 14.41 40.95 4.4 60.71 269.7 +"Turi" 11.08 6.91 13.62 2.03 51.67 14.26 39.83 4.8 59.34 290.01 +"Lorenzo" 11.1 7.03 13.22 1.85 49.34 15.38 40.22 4.5 58.36 263.08 +"Karlivans" 11.33 7.26 13.3 1.97 50.54 14.98 43.34 4.5 52.92 278.67 +"Korkizoglou" 10.86 7.07 14.81 1.94 51.16 14.96 46.07 4.7 53.05 317 +"Uldal" 11.23 6.99 13.53 1.85 50.95 15.09 43.01 4.5 60 281.7 +"Casarsa" 11.36 6.68 14.92 1.94 53.2 15.39 48.66 4.4 58.62 296.12 diff -r 000000000000 -r 46ddb0591d8b test-data/graph_file Binary file test-data/graph_file has changed diff -r 000000000000 -r 46ddb0591d8b test-data/log_file --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/log_file Thu Jan 18 07:44:37 2018 -0500 @@ -0,0 +1,2 @@ +Summary statistics report + ➔ You choose to compute : mean,sd,variance,median,quartile,decile
➔ You choose to plot : boxplot,histogram,density,pairsplot,MAplot
✓ Your process is successfull!
diff -r 000000000000 -r 46ddb0591d8b test-data/table_file --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/table_file Thu Jan 18 07:44:37 2018 -0500 @@ -0,0 +1,11 @@ +name Mean Std.Dev Variance Min Q1 Median Q3 Max D0 D1 D2 D3 D4 D5 D6 D7 D8 D9 D10 +100m 10.99805 0.26302 0.06918 10.44 10.85 10.98 11.14 11.64 10.44 10.68 10.83 10.87 10.91 10.98 11.06 11.11 11.23 11.34 11.64 +Long.jump 7.26 0.3164 0.10011 6.61 7.03 7.3 7.48 7.96 6.61 6.81 6.99 7.07 7.23 7.3 7.31 7.4 7.5 7.6 7.96 +Shot.put 14.47707 0.82443 0.67968 12.68 13.88 14.57 14.97 16.36 12.68 13.46 13.62 14.09 14.31 14.57 14.77 14.91 15.15 15.31 16.36 +High.jump 1.97683 0.08895 0.00791 1.85 1.92 1.95 2.04 2.15 1.85 1.86 1.88 1.94 1.94 1.95 1.98 2.03 2.06 2.12 2.15 +400m 49.61634 1.15345 1.33045 46.81 48.93 49.4 50.3 53.2 46.81 48.51 48.73 49.11 49.2 49.4 49.65 49.91 50.54 51.1 53.2 +110m.hurdle 14.60585 0.47179 0.22258 13.97 14.21 14.48 14.98 15.67 13.97 14.05 14.17 14.25 14.37 14.48 14.78 14.95 15.01 15.29 15.67 +Discus 44.32561 3.37784 11.40984 37.92 41.9 44.41 46.07 51.65 37.92 40.22 40.95 42.1 43.34 44.41 44.83 45.62 47.6 48.95 51.65 +Pole.vault 4.76244 0.278 0.07728 4.2 4.5 4.8 4.92 5.4 4.2 4.4 4.5 4.6 4.7 4.8 4.82 4.92 5 5.02 5.4 +Javeline 58.31659 4.82682 23.29819 50.31 55.27 58.36 60.89 70.52 50.31 52.33 54.51 55.39 56.37 58.36 59.34 60.79 61.52 63.45 70.52 +1500m 279.02488 11.67325 136.2647 262.1 271.02 278.05 285.1 317 262.1 265.42 269.54 272.74 276.31 278.05 278.82 282 287.63 291.7 317