diff plot_generic_x_y_plot.R @ 0:5118d839acae draft default tip

planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_generic_x_y_plot commit e4da8b5a999456b2b6dabdf6b8f3bfea1eba5504-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plot_generic_x_y_plot.R	Mon Apr 18 11:11:02 2016 -0400
@@ -0,0 +1,86 @@
+library('getopt')
+
+option_specification = matrix(c(
+  'input_file', 'a', 2, 'character',
+  'output_pdf_file', 'b', 2, 'character',
+  'output_png_file', 'c', 2, 'character',
+  'output_svg_file', 'd', 2, 'character',
+  'x_column_id', 'e', 2, 'integer',
+  'y_column_id', 'f', 2, 'integer',
+  'xlog', 'g', 2, 'logical',
+  'ylog', 'h', 2, 'logical',
+  'xlab', 'i', 2, 'character',
+  'ylab', 'j', 2, 'character',
+  'col', 'k', 2, 'character',
+  'pch', 'l', 2, 'integer',
+  'lim', 'm', 2, 'logical',
+  'abline', 'n', 2, 'logical',
+  'bottom_margin', 'o', 2, 'integer',
+  'left_margin', 'p', 2, 'integer',
+  'top_margin', 'q', 2, 'integer',
+  'right_margin', 'r', 2, 'integer',
+  'header','s',2,'logical'
+), byrow=TRUE, ncol=4);
+
+options = getopt(option_specification);
+
+header = TRUE
+if(!is.null(options$header)) header = options$header
+
+data = read.table(options$input_file, sep = '\t', h = header)
+
+x_column_id = 2
+if(!is.null(options$x_column_id)) x_column_id = options$x_column_id
+x_axis = data[,x_column_id]
+
+y_column_id = 3
+if(!is.null(options$y_column_id)) y_column_id = options$y_column_id
+y_axis = data[,y_column_id]
+
+xlim = c(min(x_axis),max(x_axis))
+ylim = c(min(y_axis),max(y_axis))
+if(!is.null(options$lim) && options$lim){
+  xlim = c(min(xlim,ylim), max(xlim,ylim))
+  ylim = xlim
+}
+
+
+xlab = ""
+if(!is.null(options$xlab)) xlab = options$xlab
+ylab = ""
+if(!is.null(options$ylab)) ylab = options$ylab
+
+col = 'grey25'
+if(!is.null(options$col)) col = options$col
+
+pch = 21
+if(!is.null(options$pch)) pch = options$pch
+
+log = ""
+if(!is.null(options$xlog) && options$xlog) log = paste(log,"x",sep = '')
+if(!is.null(options$ylog) && options$ylog) log = paste(log,"y",sep = '')
+
+margin = c(5,5,1,1)
+if(!is.null(options$bottom_margin)) margin[1] = options$bottom_margin
+if(!is.null(options$left_margin)) margin[2] = options$left_margin
+if(!is.null(options$top_margin)) margin[3] = options$top_margin
+if(!is.null(options$right_margin)) margin[4] = options$right_margin
+
+plot_generic_x_y_plot <- function(){
+    par(mar=margin)
+    plot(x_axis, y_axis, xlab = xlab, ylab = ylab, 
+      col = col, log = log, xlim = xlim, ylim = ylim, pch = pch)
+    if(!is.null(options$abline) && options$abline) abline(a = 0, b = 1, col = 'grey50')
+}
+
+if(!is.null(options$output_pdf_file)){
+    pdf(options$output_pdf_file)
+    plot_generic_x_y_plot()
+    dev.off()
+}
+
+if(!is.null(options$output_svg_file)){
+    svg(options$output_svg_file)
+    plot_generic_x_y_plot()
+    dev.off()
+}
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