| Next changeset 1:344ac3ca7557 (2021-11-17) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b |
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added:
boxplot.r charts.r charts.xml heatmap.r histogram.r histogramdiscrete.r test-data/boxplot.000.txt test-data/boxplot.001.txt test-data/heatmap.000.txt test-data/histogram.000.txt test-data/histogram.001.txt test-data/histogram.002.txt test-data/histogram.003.txt test-data/histogramdiscrete.000.txt test-data/tabular.txt test-data/tabular_matrix.txt test-data/tabular_single.txt test-data/tabular_small.txt |
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| diff -r 000000000000 -r a87a3773d8ed boxplot.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/boxplot.r Fri Mar 09 08:23:08 2018 -0500 |
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| @@ -0,0 +1,21 @@ +wrapper <- function(table, columns, options) { + + # initialize output list + l <- list() + + # loop through all columns + for (key in names(columns)) { + # load column data + column <- as.numeric(columns[key]) + column_data <- suppressWarnings(as.numeric(as.character(table[column][[1]]))) + + # create hist data + data <- boxplot(column_data, plot=FALSE) + + # collect vectors in list + l <- append(l, list(data$stats)) + } + + # return + return (l) +} |
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| diff -r 000000000000 -r a87a3773d8ed charts.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/charts.r Fri Mar 09 08:23:08 2018 -0500 |
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| @@ -0,0 +1,116 @@ +#!/usr/bin/Rscript + +# load getopt library +library('getopt'); + +# convert multi parameter string (i.e. key1: value, key2: value, ...) to object +split <- function(argument){ + # process parameter string + options <- list() + list <- gsub("\\s","", argument) + list <- strsplit(list, ",") + if (length(list) > 0) { + list <- list[[1]] + for (entry in list) { + pair <- strsplit(entry, ":") + if (length(pair) > 0) { + pair <- pair[[1]] + if (length(pair) == 2) { + options[[pair[1]]] <- pair[2] + } + } + } + } + return(options) +} + +# get options, using the spec as defined by the enclosed list. +spec = matrix(c( + 'workdir', 'w', 1, 'character', 'Work directory', + 'module', 'm', 1, 'character', 'Module name', + 'input', 'i', 1, 'character', 'Input tabular file', + 'columns', 'c', 1, 'character', 'Columns string', + 'settings', 's', 1, 'character', 'Settings string', + 'output', 'o', 1, 'character', 'Output tabular file', + 'help', 'h', 0, '', 'Help', + 'verbose', 'v', 0, '', 'Verbose' +), byrow=TRUE, ncol=5); +opt = getopt(spec); + +# show help +if ( !is.null(opt$help) || + is.null(opt$module) || + is.null(opt$input) || + is.null(opt$columns) || + is.null(opt$output)) { + cat(getopt(spec, usage=TRUE)) + q(status=1); +} + +# read columns/settings +columns = split(opt$columns) +settings = split(opt$settings) + +# read table +table <- read.table(opt$input, comment.char='#', fill=TRUE) + +# identify module file +module_file = paste(opt$workdir, opt$module, '.r', sep='') + +# source module +source(module_file) + +# run module +l = wrapper (table, columns, settings) + +# header +header_title <- '# title - Chart Utilities (charts)' +header_date <- paste('# date -', Sys.time(), sep=' ') +header_module <- paste('# module -', opt$module, sep=' ') +header_settings <- paste('# settings -', opt$settings, sep=' ') +header_columns <- paste('# columns -', opt$columns, sep=' ') + +# check result +if (length(l) > 0) { + # print details + if (!is.null(opt$verbose)) { + print ('Columns:') + print (columns) + print ('Settings:') + print (settings) + print ('Result:') + print (l) + } + + # create output file + output <- file(opt$output, open='wt') + + # write header + writeLines('#', output) + writeLines(header_title, output) + writeLines(header_date, output) + writeLines(header_module, output) + writeLines(header_settings, output) + writeLines(header_columns, output) + writeLines('#', output) + + # pad columns + rows <- max(unlist(lapply(l, length))) + padded <- lapply(l, function(col) { + length(col) = rows; + col + }) + + # write table + write.table(padded, file=output, row.names=FALSE, col.names = FALSE, quote=FALSE, sep='\t') + + # close file + close(output) +} else { + # print details + print ('Columns:') + print (columns) + print ('Settings:') + print (settings) + print ('No output generated.') +} \ No newline at end of file |
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| diff -r 000000000000 -r a87a3773d8ed charts.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/charts.xml Fri Mar 09 08:23:08 2018 -0500 |
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| @@ -0,0 +1,90 @@ +<tool id="charts" name="Charts" version="1.0.1" hidden="true"> + <description>wrapper for R</description> + <requirements> + <requirement type="package" version="1.20.0">r-getopt</requirement> + <requirement type="package" version="1.2-12">r-matrix</requirement> + </requirements> + <command detect_errors="aggressive"> +<![CDATA[ + Rscript '$__tool_directory__/charts.r' + -w '$__tool_directory__/' + -m ${module} + -i '${input}' + -c '${columns}' + -s '${settings}' + -o '${output}' +]]> + </command> + <inputs> + <param name="input" type="data" label="Input dataset" format="tabular" /> + <param name="module" type="select" label="R-script"> + <option value="boxplot">boxplot</option> + <option value="heatmap">heatmap</option> + <option value="histogram">histogram</option> + <option value="histogramdiscrete">histogramdiscrete</option> + </param> + <param name="columns" type="text" area="true" label="Columns string (i.e key1: column, key2: column)" value=""/> + <param name="settings" type="text" area="true" label="Options string (i.e key1: value, key2: value)" value=""/> + </inputs> + <outputs> + <data name="output" format="tabular" /> + </outputs> + <tests> + <test> + <param name="input" value="tabular.txt" /> + <param name="module" value="histogram" /> + <param name="columns" value="key1: 2" /> + <param name="settings" value="" /> + <output name="output" file="histogram.000.txt" lines_diff="2"/> + </test> + <test> + <param name="input" value="tabular.txt" /> + <param name="module" value="histogram" /> + <param name="columns" value="key1: 2, key2: 3, key3: 4" /> + <param name="settings" value="" /> + <output name="output" file="histogram.001.txt" lines_diff="2"/> + </test> + <test> + <param name="input" value="tabular.txt" /> + <param name="module" value="histogram" /> + <param name="columns" value="key1: 6" /> + <param name="settings" value="" /> + <output name="output" file="histogram.002.txt" lines_diff="2"/> + </test> + <test> + <param name="input" value="tabular_single.txt" /> + <param name="module" value="histogram" /> + <param name="columns" value="key1: 1" /> + <param name="settings" value="" /> + <output name="output" file="histogram.003.txt" lines_diff="2"/> + </test> + <test> + <param name="input" value="tabular.txt" /> + <param name="module" value="boxplot" /> + <param name="columns" value="key1: 2" /> + <param name="settings" value="" /> + <output name="output" file="boxplot.000.txt" lines_diff="2"/> + </test> + <test> + <param name="input" value="tabular.txt" /> + <param name="module" value="boxplot" /> + <param name="columns" value="key1: 2, key2: 3, key3: 4" /> + <param name="settings" value="" /> + <output name="output" file="boxplot.001.txt" lines_diff="2"/> + </test> + <test> + <param name="input" value="tabular_matrix.txt" /> + <param name="module" value="histogramdiscrete" /> + <param name="columns" value="key1: 1, key2: 2, key3: 3" /> + <param name="settings" value="" /> + <output name="output" file="histogramdiscrete.000.txt" lines_diff="2"/> + </test> + <test> + <param name="input" value="tabular_matrix.txt" ftype="tabular" /> + <param name="module" value="heatmap" /> + <param name="columns" value="key1: 1, key2: 2, key3: 3" /> + <param name="settings" value="" /> + <output name="output" file="heatmap.000.txt" lines_diff="2"/> + </test> + </tests> +</tool> |
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| diff -r 000000000000 -r a87a3773d8ed heatmap.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/heatmap.r Fri Mar 09 08:23:08 2018 -0500 |
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| @@ -0,0 +1,97 @@ +# load sparse matrix package +suppressPackageStartupMessages(library('Matrix')) + +# access a numeric column +get_numeric <- function(table, column_key) { + column <- as.numeric(column_key) + column_data <- suppressWarnings(as.numeric(as.character(table[column][[1]]))) + return (c(column_data)) +} + +# access a label column +get_label <- function(table, column_key) { + column <- as.numeric(column_key) + column_data <- as.character(table[column][[1]]) + return (c(column_data)) +} + +# inflate three columns into matrix +matrify <- function (data) { + if (ncol(data) != 3) + stop('Data frame must have three column format') + plt <- data[, 1] + spc <- data[, 2] + abu <- data[, 3] + plt.codes <- levels(factor(plt)) + spc.codes <- levels(factor(spc)) + taxa <- Matrix(0, nrow=length(plt.codes), ncol=length(spc.codes), sparse=TRUE) + row <- match(plt, plt.codes) + col <- match(spc, spc.codes) + for (i in 1:length(abu)) { + taxa[row[i], col[i]] <- abu[i] + } + colnames(taxa) <- spc.codes + rownames(taxa) <- plt.codes + taxa +} + +# flatten data.frame into three column format +flatten <- function(my_matrix) { + summ <-summary(my_matrix) + summ <- data.frame(i=rownames(my_matrix)[summ$i], j=colnames(my_matrix)[summ$j], x=summ$x) + summ +} + +# wrapper +wrapper <- function(table, columns, options) { + + # initialize output list + l <- list() + + # get number of columns + n = length(columns) + + # consistency check + if (n %% 3 != 0) { + print ('heatmap::wrapper() - Data not consistent (n mod 3 != 0)') + return (l) + } + + # create index sequence + index = seq(1, n, by=3) + + # get keys + keys = names(columns) + + # loop through blocks + for (i in index) { + # create columns + ci <- get_label(table, columns[keys[i]]) + cj <- get_label(table, columns[keys[i+1]]) + cx <- get_numeric(table, columns[keys[i+2]]) + + # create a frame from columns + my_frame <- data.frame(ci=ci, cj=cj, cx=cx) + + # create matrix out of the frame + my_matrix <- matrify(my_frame) + + # create/cluster matrix + row_order <- hclust(dist(my_matrix))$order + col_order <- hclust(dist(t(my_matrix)))$order + + # reorder matrix + my_matrix <- my_matrix[row_order, col_order] + + # transform back to three columns + my_flatmatrix = flatten(my_matrix) + + # append to result list + l <- append(l, list(my_flatmatrix$i)) + l <- append(l, list(my_flatmatrix$j)) + l <- append(l, list(my_flatmatrix$x)) + } + + # return + return (l) +} |
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| diff -r 000000000000 -r a87a3773d8ed histogram.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/histogram.r Fri Mar 09 08:23:08 2018 -0500 |
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| @@ -0,0 +1,45 @@ +# wrapper +wrapper <- function(table, columns, options) { + + # initialize output list + l <- list() + + # loop through all columns + m <- list() + for (key in names(columns)) { + # load column data + column <- as.numeric(columns[key]) + column_data <- suppressWarnings(as.numeric(as.character(table[column][[1]]))) + + # collect vectors in list + m <- append(m, list(column_data)) + } + + # identify optimal breaks + hist_data <- hist(unlist(m), plot=FALSE) + breaks <- hist_data$breaks; + + # add as first column + l <- append(l, list(breaks[2: length(breaks)])) + + # loop through all columns + for (key in seq(m)) { + # load column data + column_data <- m[[key]] + + # create hist data + hist_data <- hist(column_data, breaks=breaks, plot=FALSE) + + # normalize densities + count_sum <- sum(hist_data$counts) + if (count_sum > 0) { + hist_data$counts = hist_data$counts / count_sum + } + + # collect vectors in list + l <- append(l, list(hist_data$counts)) + } + + # return + return (l) +} |
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| diff -r 000000000000 -r a87a3773d8ed histogramdiscrete.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/histogramdiscrete.r Fri Mar 09 08:23:08 2018 -0500 |
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| @@ -0,0 +1,54 @@ +# wrapper +wrapper <- function(table, columns, options) { + + # initialize output list + l <- list() + + # loop through all columns + m <- list() + for (key in names(columns)) { + # load column data + column <- as.numeric(columns[key]) + + # ensure string column + column_data <- as.character(table[column][[1]]) + + # collect vectors in list + m <- append(m, list(column_data)) + } + + # get alphabetically sorted bins + bins <- sort(unique(unlist(m))) + + # add first column + l <- append(l, list(bins)) + + # loop through all columns + for (key in seq(m)) { + # reset bins + bins = sapply(bins, function(v) { 0 }) + + # load column data + column_data <- m[[key]] + + # create hist data + table_data <- table(column_data) + + # transfer counts to bins + for (id in names(table_data)) { + bins[id] <- table_data[id] + } + + # normalize densities + total <- length(column_data) + if (total > 0) { + bins = bins / total + } + + # collect vectors in list + l <- append(l, list(bins)) + } + + # return + return (l) +} |
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| diff -r 000000000000 -r a87a3773d8ed test-data/boxplot.000.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/boxplot.000.txt Fri Mar 09 08:23:08 2018 -0500 |
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| @@ -0,0 +1,12 @@ +# +# title - Chart Utilities (charts) +# date - 2014-04-25 19:44:41 +# module - boxplot +# settings - +# columns - key1: 2 +# +0 +24 +50 +75 +100 |
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| diff -r 000000000000 -r a87a3773d8ed test-data/boxplot.001.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/boxplot.001.txt Fri Mar 09 08:23:08 2018 -0500 |
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| @@ -0,0 +1,12 @@ +# +# title - Chart Utilities (charts) +# date - 2014-04-25 19:45:09 +# module - boxplot +# settings - +# columns - key1: 2, key2: 3, key3: 4 +# +0 1 0 +24 20 17 +50 47.5 42.5 +75 74 69.5 +100 100 100 |
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| diff -r 000000000000 -r a87a3773d8ed test-data/heatmap.000.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/heatmap.000.txt Fri Mar 09 08:23:08 2018 -0500 |
| b |
| b'@@ -0,0 +1,6000 @@\n+#\n+# title - Chart Utilities (charts)\n+# date - 2018-03-09 08:30:44\n+# module - heatmap\n+# settings - \n+# columns - key1: 1, key2: 2, key3: 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|
| b |
| diff -r 000000000000 -r a87a3773d8ed test-data/histogram.000.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/histogram.000.txt Fri Mar 09 08:23:08 2018 -0500 |
| b |
| @@ -0,0 +1,17 @@ +# +# title - Chart Utilities (charts) +# date - 2014-05-08 14:47:25 +# module - histogram +# settings - +# columns - key1: 2 +# +10 0.15 +20 0.06 +30 0.15 +40 0.07 +50 0.07 +60 0.09 +70 0.11 +80 0.1 +90 0.07 +100 0.13 |
| b |
| diff -r 000000000000 -r a87a3773d8ed test-data/histogram.001.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/histogram.001.txt Fri Mar 09 08:23:08 2018 -0500 |
| b |
| @@ -0,0 +1,17 @@ +# +# title - Chart Utilities (charts) +# date - 2014-05-08 14:48:20 +# module - histogram +# settings - +# columns - key1: 2, key2: 3, key3: 4 +# +10 0.15 0.14 0.15 +20 0.06 0.12 0.19 +30 0.15 0.08 0.07 +40 0.07 0.09 0.08 +50 0.07 0.11 0.09 +60 0.09 0.08 0.12 +70 0.11 0.1 0.06 +80 0.1 0.09 0.06 +90 0.07 0.09 0.09 +100 0.13 0.1 0.09 |
| b |
| diff -r 000000000000 -r a87a3773d8ed test-data/histogram.002.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/histogram.002.txt Fri Mar 09 08:23:08 2018 -0500 |
| b |
| @@ -0,0 +1,17 @@ +# +# title - Chart Utilities (charts) +# date - 2018-01-31 00:52:34 +# module - histogram +# settings - +# columns - key1: 6 +# +10 0.1 +20 0.13 +30 0.11 +40 0.11 +50 0.05 +60 0.1 +70 0.12 +80 0.13 +90 0.08 +100 0.07 |
| b |
| diff -r 000000000000 -r a87a3773d8ed test-data/histogram.003.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/histogram.003.txt Fri Mar 09 08:23:08 2018 -0500 |
| b |
| @@ -0,0 +1,26 @@ +# +# title - Chart Utilities (charts) +# date - 2018-01-31 00:52:47 +# module - histogram +# settings - +# columns - key1: 1 +# +10 0.845934807043837 +20 0.126988884725865 +30 0.0208067940552017 +40 0.00467091295116773 +50 0.00104908205320345 +60 0.000274759585362808 +70 7.49344323716748e-05 +80 7.49344323716748e-05 +90 0 +100 2.49781441238916e-05 +110 2.49781441238916e-05 +120 4.99562882477832e-05 +130 0 +140 0 +150 0 +160 0 +170 0 +180 0 +190 2.49781441238916e-05 |
| b |
| diff -r 000000000000 -r a87a3773d8ed test-data/histogramdiscrete.000.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/histogramdiscrete.000.txt Fri Mar 09 08:23:08 2018 -0500 |
| b |
| b'@@ -0,0 +1,1790 @@\n+#\n+# title - Chart Utilities (charts)\n+# date - 2014-05-09 00:48:18\n+# module - histogramdiscrete\n+# settings - \n+# columns - key1: 1, key2: 2, key3: 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|
| b |
| diff -r 000000000000 -r a87a3773d8ed test-data/tabular.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tabular.txt Fri Mar 09 08:23:08 2018 -0500 |
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| diff -r 000000000000 -r a87a3773d8ed test-data/tabular_matrix.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tabular_matrix.txt Fri Mar 09 08:23:08 2018 -0500 |
| b |
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|
| b |
| diff -r 000000000000 -r a87a3773d8ed test-data/tabular_single.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tabular_single.txt Fri Mar 09 08:23:08 2018 -0500 |
| b |
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|
| b |
| diff -r 000000000000 -r a87a3773d8ed test-data/tabular_small.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tabular_small.txt Fri Mar 09 08:23:08 2018 -0500 |
| b |
| @@ -0,0 +1,1 @@ +label1 labela 43 14 75 95 85 57 62 80 94 57 label2 labela 33 100 32 20 17 50 24 85 0 33 label3 labela 5 60 46 54 34 89 44 43 54 86 label4 labela 35 73 40 58 21 23 38 45 1 2 label5 labele 45 3 36 35 5 15 49 20 80 31 label6 labelf 6 84 89 72 30 79 45 23 20 59 label7 labelg 26 36 69 84 38 14 11 33 23 1 label1 labelh 100 83 27 46 14 1 34 29 25 35 label9 labeli 53 28 22 95 65 45 47 38 18 55 label10 labelj 6 72 25 56 75 64 79 88 67 29 label1 labelk 78 12 98 12 7 5 83 29 22 50 label12 labell 18 37 77 86 37 80 71 77 12 40 label13 labelm 79 51 54 82 1 84 85 10 53 10 label14 labeln 97 98 63 57 6 52 68 17 78 86 \ No newline at end of file |