| Previous changeset 1:fbedb212982d (2024-02-08) |
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Commit message:
planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit f8dffb887b68fdc2c9b35f30676539b8396abd54 |
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modified:
ez_histograms.R ez_histograms.xml |
| b |
| diff -r fbedb212982d -r d375c9df9c34 ez_histograms.R --- a/ez_histograms.R Thu Feb 08 02:15:11 2024 +0000 +++ b/ez_histograms.R Thu Nov 07 15:40:40 2024 +0000 |
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| b'@@ -5,121 +5,125 @@\n library(psych)\n library(optparse)\n \n-options(show.error.messages = FALSE,\n- error = function() {\n- cat(geterrmessage(), file = stderr())\n- q("no", 1, FALSE)\n- }\n+options(\n+ show.error.messages = FALSE,\n+ error = function() {\n+ cat(geterrmessage(), file = stderr())\n+ q("no", 1, FALSE)\n+ }\n )\n \n loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")\n warnings()\n \n option_list <- list(\n- make_option(\n- c("-f", "--file"),\n- default = NA,\n- type = "character",\n- help = "Input file that contains count values to transform"\n- ),\n- make_option(\n- c("-d", "--profile"),\n- default = "count",\n- type = "character",\n- help = "Whether y-axis shows absolute counts or density: \'count\' or \'density\' [default : \'%default\' ]"\n- ),\n- make_option(\n- "--xscale",\n- default = "cartesian",\n- type = "character",\n- help = "Whether x-axis is \'cartesian\', \'log2\' or \'log10\' [default : \'%default\' ]"\n- ),\n- make_option(\n- "--yscale",\n- default = "cartesian",\n- type = "character",\n- help = "Whether y-axis is \'cartesian\', \'log2\' or \'log10\' [default : \'%default\' ]"\n- ),\n- make_option(\n- c("-p", "--pdf"),\n- default = "histograms.pdf",\n- type = "character",\n- help = "Output pdf file name [default : \'%default\' ]"\n- ),\n- make_option(\n- c("-s", "--summary"),\n- default = "summary.tsv",\n- type = "character",\n- help = "statistics summary file name [default : \'%default\' ]"\n- )\n+ make_option(\n+ c("-f", "--file"),\n+ default = NA,\n+ type = "character",\n+ help = "Input file that contains count values to transform"\n+ ),\n+ make_option(\n+ c("-d", "--profile"),\n+ default = "count",\n+ type = "character",\n+ help = "Whether y-axis shows absolute counts or density: \'count\' or \'density\' [default : \'%default\' ]"\n+ ),\n+ make_option(\n+ "--xscale",\n+ default = "cartesian",\n+ type = "character",\n+ help = "Whether x-axis is \'cartesian\', \'log2\' or \'log10\' [default : \'%default\' ]"\n+ ),\n+ make_option(\n+ "--yscale",\n+ default = "cartesian",\n+ type = "character",\n+ help = "Whether y-axis is \'cartesian\', \'log2\' or \'log10\' [default : \'%default\' ]"\n+ ),\n+ make_option(\n+ c("-p", "--pdf"),\n+ default = "histograms.pdf",\n+ type = "character",\n+ help = "Output pdf file name [default : \'%default\' ]"\n+ ),\n+ make_option(\n+ c("-s", "--summary"),\n+ default = "summary.tsv",\n+ type = "character",\n+ help = "statistics summary file name [default : \'%default\' ]"\n+ )\n )\n \n opt <- parse_args(OptionParser(option_list = option_list),\n- args = commandArgs(trailingOnly = TRUE))\n+ args = commandArgs(trailingOnly = TRUE)\n+)\n \n plot_histograms <- function(mdata, profile = "count", xscale = "cartesian", yscale = "cartesian", bins = 30) {\n- if (profile == "count") {\n- # count histogram\n- p <- ggplot(mdata, aes(x = value, fill = variable, color = variable, y = after_stat(count)), show.legend = FALSE) +\n- geom_histogram(bins = bins) + theme(legend.position = "none")\n- if (xscale == "cartesian") {\n- if (yscale == "log2") {\n- p <- p + scale_y_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))\n- } else {\n- if (yscale == "log10") {\n- p <- p + scale_y_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))\n+ if (profile == "count") {\n+ # count histogram\n+ p <- ggplot(mdata, aes(x = value, fill = variable, color = variable, y = after_stat(count)), show.legend = FALSE) +\n+ geom_histogram(bins = bins) +\n+ theme(legend.position = "none")\n+ if (xscale == "cartesian") {\n+ if (yscale == "log2") {\n+ p <- p + scale_y_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))\n+ } else {\n+ '..b'x_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))\n+ if (yscale == "log2") {\n+ p <- p + scale_y_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))\n+ } else {\n+ if (yscale == "log10") {\n+ p <- p + scale_y_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))\n+ }\n+ }\n }\n- }\n+ if (xscale == "log10") {\n+ p <- p + scale_x_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))\n+ if (yscale == "log2") {\n+ p <- p + scale_y_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))\n+ } else {\n+ if (yscale == "log10") {\n+ p <- p + scale_y_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))\n+ }\n+ }\n+ }\n }\n- if (xscale == "log10") {\n- p <- p + scale_x_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))\n- if (yscale == "log2") {\n- p <- p + scale_y_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))\n- } else {\n- if (yscale == "log10") {\n- p <- p + scale_y_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))\n+\n+ if (profile == "density") {\n+ # density histogram\n+ p <- ggplot(mdata, aes(x = value, fill = variable, color = variable)) +\n+ geom_density() +\n+ theme(legend.position = "none")\n+ if (xscale == "log2") {\n+ p <- p + scale_x_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))\n }\n- }\n+ if (xscale == "log10") {\n+ p <- p + scale_x_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))\n+ }\n }\n- }\n-\n- if (profile == "density") {\n- # density histogram\n- p <- ggplot(mdata, aes(x = value, fill = variable, color = variable)) +\n- geom_density() + theme(legend.position = "none")\n- if (xscale == "log2") {\n- p <- p + scale_x_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))\n- }\n- if (xscale == "log10") {\n- p <- p + scale_x_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))\n- }\n- }\n- return(p)\n+ return(p)\n }\n \n test_header <- function(file) {\n- data <- read.delim(file = file, header = FALSE, row.names = 1, nrows = 2)\n- if (all(is.na(as.numeric(data[1, seq_len(ncol(data))])))) {\n- return(TRUE)\n- } else {\n- return(FALSE)\n- }\n+ data <- read.delim(file = file, header = FALSE, row.names = 1, nrows = 2)\n+ if (all(is.na(as.numeric(data[1, seq_len(ncol(data))])))) {\n+ return(TRUE)\n+ } else {\n+ return(FALSE)\n+ }\n }\n \n ##### prepare input data\n \n data <- read.delim(file = opt$file, header = test_header(opt$file))\n-data <- data %>% select(where(is.numeric)) # remove non numeric columns\n+data <- data %>% select(where(is.numeric)) # remove non numeric columns\n mdata <- melt(data)\n \n ##### main\n@@ -132,23 +136,23 @@\n # determine optimal width for the graph\n width <- length(data)\n width <- case_when(\n- width == 1 ~ 14 / 3,\n- width == 2 ~ (2 / 3) * 14,\n- TRUE ~ 14\n+ width == 1 ~ 14 / 3,\n+ width == 2 ~ (2 / 3) * 14,\n+ TRUE ~ 14\n )\n # determine optimal height for the graph\n height <- length(data)\n height <- case_when(\n- height <= 3 ~ 3,\n- height <= 6 ~ 6,\n- TRUE ~ (floor(height / 3) + 1) * 3\n+ height <= 3 ~ 3,\n+ height <= 6 ~ 6,\n+ TRUE ~ (floor(height / 3) + 1) * 3\n )\n # determine optimal number of col for the graph\n ncol <- length(data)\n ncol <- case_when(\n- ncol == 1 ~ 1,\n- ncol == 2 ~ 2,\n- TRUE ~ 3\n+ ncol == 1 ~ 1,\n+ ncol == 2 ~ 2,\n+ TRUE ~ 3\n )\n pdf(opt$pdf, width = width, height = height)\n print(p + facet_wrap(~variable, ncol = ncol, scales = "free"))\n' |
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| diff -r fbedb212982d -r d375c9df9c34 ez_histograms.xml --- a/ez_histograms.xml Thu Feb 08 02:15:11 2024 +0000 +++ b/ez_histograms.xml Thu Nov 07 15:40:40 2024 +0000 |
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| @@ -1,9 +1,14 @@ <tool id="ez_histograms" name="ez_histograms" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <macros> <token name="@TOOL_VERSION@">3.4.4</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@PROFILE@">23.0</token> </macros> + + <xrefs> + <xref type="bio.tools">ez_histograms</xref> + </xrefs> + <requirements> <requirement type="package" version="3.4.4">r-ggplot2</requirement> <requirement type="package" version="1.4.4">r-reshape2</requirement> |