# HG changeset patch
# User saskia-hiltemann
# Date 1446216409 14400
# Node ID d43075b3e107e69a331f5cfb583907c29371da8a
Uploaded
diff -r 000000000000 -r d43075b3e107 r_wrapper.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/r_wrapper.sh Fri Oct 30 10:46:49 2015 -0400
@@ -0,0 +1,23 @@
+#!/bin/sh
+
+### Run R providing the R script in $1 as standard input and passing
+### the remaining arguments on the command line
+
+# Function that writes a message to stderr and exits
+function fail
+{
+ echo "$@" >&2
+ exit 1
+}
+
+# Ensure R executable is found
+which R > /dev/null || fail "'R' is required by this tool but was not found on path"
+
+# Extract first argument
+infile=$1; shift
+
+# Ensure the file exists
+test -f $infile || fail "R input file '$infile' does not exist"
+
+# Invoke R passing file named by first argument to stdin
+R --vanilla --slave $* < $infile
diff -r 000000000000 -r d43075b3e107 test-data/2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2.tabular Fri Oct 30 10:46:49 2015 -0400
@@ -0,0 +1,10 @@
+1 68 4.1
+2 71 4.6
+3 62 3.8
+4 75 4.4
+5 58 3.2
+6 60 3.1
+7 67 3.8
+8 68 4.1
+9 71 4.3
+10 69 3.7
diff -r 000000000000 -r d43075b3e107 test-data/XY_Plot_1_multi_out.pdf
Binary file test-data/XY_Plot_1_multi_out.pdf has changed
diff -r 000000000000 -r d43075b3e107 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Fri Oct 30 10:46:49 2015 -0400
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diff -r 000000000000 -r d43075b3e107 xy_example.jpg
Binary file xy_example.jpg has changed
diff -r 000000000000 -r d43075b3e107 xy_plot.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/xy_plot.xml Fri Oct 30 10:46:49 2015 -0400
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+ for multiple series and graph types and multiple output types
+
+ R
+ fontconfig
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+ r_wrapper.sh $script_file
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+ ## Setup R error handling to go to stderr
+ options( show.error.messages=F,
+ error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+ ## Determine range of all series in the plot
+ xrange = c( NULL, NULL )
+ yrange = c( NULL, NULL )
+ #for $i, $s in enumerate( $series )
+ s${i} = read.table( "${s.input.file_name}" )
+ x${i} = s${i}[,${s.xcol}]
+ y${i} = s${i}[,${s.ycol}]
+ xrange = range( x${i}, xrange )
+ yrange = range( y${i}, yrange )
+ #end for
+ ## Open output PDF file
+ #if $ftype.value == "pdf"
+ pdf("outfile.pdf")
+ #else
+ "${ftype}"( "outfile.${ftype}" , type="cairo")
+ #end if
+ ## Dummy plot for axis / labels
+ plot( NULL, type="n", xlim=xrange, ylim=yrange, main="${main}", xlab="${xlab}", ylab="${ylab}" )
+ ## Plot each series
+ #for $i, $s in enumerate( $series )
+ #if $s.series_type['type'] == "line"
+ lines( x${i}, y${i}, lty=${s.series_type.lty}, lwd=${s.series_type.lwd}, col=${s.series_type.col} )
+ #elif $s.series_type.type == "points"
+ points( x${i}, y${i}, pch=${s.series_type.pch}, cex=${s.series_type.cex}, col=${s.series_type.col} )
+ #end if
+ #end for
+ ## Close the PDF file
+ devname = dev.off()
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+ (ftype == 'pdf')
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+ (ftype == 'png')
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+ (ftype == 'tiff')
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+.. class:: infomark
+
+This tool allows you to plot values contained in columns of a dataset against each other and also allows you to have different series corresponding to the same or different datasets in one plot.
+
+-----
+
+.. class:: warningmark
+
+This tool throws an error if the columns selected for plotting are absent or are not numeric and also if the lengths of these columns differ.
+
+-----
+
+**Example**
+
+Input file::
+
+ 1 68 4.1
+ 2 71 4.6
+ 3 62 3.8
+ 4 75 4.4
+ 5 58 3.2
+ 6 60 3.1
+ 7 67 3.8
+ 8 68 4.1
+ 9 71 4.3
+ 10 69 3.7
+
+Create a two series XY plot on the above data:
+
+- Series 1: Red Dashed-Line plot between columns 1 and 2
+- Series 2: Blue Circular-Point plot between columns 3 and 2
+
+.. image:: xy_example.jpg
+
+