Mercurial > repos > artbio > ez_histograms

changeset 2:d375c9df9c34 draft default tip

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planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit f8dffb887b68fdc2c9b35f30676539b8396abd54
author artbio
date Thu, 07 Nov 2024 15:40:40 +0000
parents fbedb212982d
children
files ez_histograms.R ez_histograms.xml
diffstat 2 files changed, 110 insertions(+), 101 deletions(-) [+]
line wrap: on
line diff
--- a/ez_histograms.R	Thu Feb 08 02:15:11 2024 +0000
+++ b/ez_histograms.R	Thu Nov 07 15:40:40 2024 +0000
@@ -5,121 +5,125 @@
 library(psych)
 library(optparse)
 
-options(show.error.messages = FALSE,
-  error = function() {
-    cat(geterrmessage(), file = stderr())
-    q("no", 1, FALSE)
-  }
+options(
+    show.error.messages = FALSE,
+    error = function() {
+        cat(geterrmessage(), file = stderr())
+        q("no", 1, FALSE)
+    }
 )
 
 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
 warnings()
 
 option_list <- list(
-  make_option(
-    c("-f", "--file"),
-    default = NA,
-    type = "character",
-    help = "Input file that contains count values to transform"
-  ),
-  make_option(
-    c("-d", "--profile"),
-    default = "count",
-    type = "character",
-    help = "Whether y-axis shows absolute counts or density: 'count' or 'density' [default : '%default' ]"
-  ),
-  make_option(
-    "--xscale",
-    default = "cartesian",
-    type = "character",
-    help = "Whether x-axis is 'cartesian', 'log2' or 'log10' [default : '%default' ]"
-  ),
-  make_option(
-    "--yscale",
-    default = "cartesian",
-    type = "character",
-    help = "Whether y-axis is 'cartesian', 'log2' or 'log10' [default : '%default' ]"
-  ),
-  make_option(
-    c("-p", "--pdf"),
-    default = "histograms.pdf",
-    type = "character",
-    help = "Output pdf file name [default : '%default' ]"
-  ),
-  make_option(
-    c("-s", "--summary"),
-    default = "summary.tsv",
-    type = "character",
-    help = "statistics summary file name [default : '%default' ]"
-  )
+    make_option(
+        c("-f", "--file"),
+        default = NA,
+        type = "character",
+        help = "Input file that contains count values to transform"
+    ),
+    make_option(
+        c("-d", "--profile"),
+        default = "count",
+        type = "character",
+        help = "Whether y-axis shows absolute counts or density: 'count' or 'density' [default : '%default' ]"
+    ),
+    make_option(
+        "--xscale",
+        default = "cartesian",
+        type = "character",
+        help = "Whether x-axis is 'cartesian', 'log2' or 'log10' [default : '%default' ]"
+    ),
+    make_option(
+        "--yscale",
+        default = "cartesian",
+        type = "character",
+        help = "Whether y-axis is 'cartesian', 'log2' or 'log10' [default : '%default' ]"
+    ),
+    make_option(
+        c("-p", "--pdf"),
+        default = "histograms.pdf",
+        type = "character",
+        help = "Output pdf file name [default : '%default' ]"
+    ),
+    make_option(
+        c("-s", "--summary"),
+        default = "summary.tsv",
+        type = "character",
+        help = "statistics summary file name [default : '%default' ]"
+    )
 )
 
 opt <- parse_args(OptionParser(option_list = option_list),
-                  args = commandArgs(trailingOnly = TRUE))
+    args = commandArgs(trailingOnly = TRUE)
+)
 
 plot_histograms <- function(mdata, profile = "count", xscale = "cartesian", yscale = "cartesian", bins = 30) {
-  if (profile == "count") {
-    # count histogram
-    p <- ggplot(mdata, aes(x = value, fill = variable, color = variable, y = after_stat(count)), show.legend = FALSE) +
-      geom_histogram(bins = bins) + theme(legend.position = "none")
-    if (xscale == "cartesian") {
-      if (yscale == "log2") {
-        p <- p + scale_y_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))
-      } else {
-        if (yscale == "log10") {
-          p <- p + scale_y_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))
+    if (profile == "count") {
+        # count histogram
+        p <- ggplot(mdata, aes(x = value, fill = variable, color = variable, y = after_stat(count)), show.legend = FALSE) +
+            geom_histogram(bins = bins) +
+            theme(legend.position = "none")
+        if (xscale == "cartesian") {
+            if (yscale == "log2") {
+                p <- p + scale_y_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))
+            } else {
+                if (yscale == "log10") {
+                    p <- p + scale_y_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))
+                }
+            }
         }
-      }
-    }
-    if (xscale == "log2") {
-      p <- p + scale_x_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))
-      if (yscale == "log2") {
-        p <- p + scale_y_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))
-      } else {
-        if (yscale == "log10") {
-          p <- p + scale_y_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))
+        if (xscale == "log2") {
+            p <- p + scale_x_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))
+            if (yscale == "log2") {
+                p <- p + scale_y_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))
+            } else {
+                if (yscale == "log10") {
+                    p <- p + scale_y_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))
+                }
+            }
         }
-      }
+        if (xscale == "log10") {
+            p <- p + scale_x_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))
+            if (yscale == "log2") {
+                p <- p + scale_y_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))
+            } else {
+                if (yscale == "log10") {
+                    p <- p + scale_y_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))
+                }
+            }
+        }
     }
-    if (xscale == "log10") {
-      p <- p + scale_x_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))
-      if (yscale == "log2") {
-        p <- p + scale_y_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))
-      } else {
-        if (yscale == "log10") {
-          p <- p + scale_y_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))
+
+    if (profile == "density") {
+        # density histogram
+        p <- ggplot(mdata, aes(x = value, fill = variable, color = variable)) +
+            geom_density() +
+            theme(legend.position = "none")
+        if (xscale == "log2") {
+            p <- p + scale_x_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))
         }
-      }
+        if (xscale == "log10") {
+            p <- p + scale_x_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))
+        }
     }
-  }
-
-  if (profile == "density") {
-    # density histogram
-    p <- ggplot(mdata, aes(x = value, fill = variable, color = variable)) +
-      geom_density() + theme(legend.position = "none")
-    if (xscale == "log2") {
-      p <- p + scale_x_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))
-    }
-    if (xscale == "log10") {
-      p <- p + scale_x_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))
-    }
-  }
-  return(p)
+    return(p)
 }
 
 test_header <- function(file) {
-  data <- read.delim(file = file, header = FALSE, row.names = 1, nrows = 2)
-  if (all(is.na(as.numeric(data[1, seq_len(ncol(data))])))) {
-    return(TRUE)
-  } else {
-    return(FALSE)
-  }
+    data <- read.delim(file = file, header = FALSE, row.names = 1, nrows = 2)
+    if (all(is.na(as.numeric(data[1, seq_len(ncol(data))])))) {
+        return(TRUE)
+    } else {
+        return(FALSE)
+    }
 }
 
 ##### prepare input data
 
 data <- read.delim(file = opt$file, header = test_header(opt$file))
-data <- data %>% select(where(is.numeric))  # remove non numeric columns
+data <- data %>% select(where(is.numeric)) # remove non numeric columns
 mdata <- melt(data)
 
 ##### main
@@ -132,23 +136,23 @@
 # determine optimal width for the graph
 width <- length(data)
 width <- case_when(
-  width == 1 ~ 14 / 3,
-  width == 2 ~ (2 / 3) * 14,
-  TRUE ~ 14
+    width == 1 ~ 14 / 3,
+    width == 2 ~ (2 / 3) * 14,
+    TRUE ~ 14
 )
 # determine optimal height for the graph
 height <- length(data)
 height <- case_when(
-  height <= 3 ~ 3,
-  height <= 6 ~ 6,
-  TRUE ~ (floor(height / 3) + 1) * 3
+    height <= 3 ~ 3,
+    height <= 6 ~ 6,
+    TRUE ~ (floor(height / 3) + 1) * 3
 )
 # determine optimal number of col for the graph
 ncol <- length(data)
 ncol <- case_when(
-  ncol == 1 ~ 1,
-  ncol == 2 ~ 2,
-  TRUE ~ 3
+    ncol == 1 ~ 1,
+    ncol == 2 ~ 2,
+    TRUE ~ 3
 )
 pdf(opt$pdf, width = width, height = height)
 print(p + facet_wrap(~variable, ncol = ncol, scales = "free"))
--- a/ez_histograms.xml	Thu Feb 08 02:15:11 2024 +0000
+++ b/ez_histograms.xml	Thu Nov 07 15:40:40 2024 +0000
@@ -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>