# HG changeset patch # User devteam # Date 1481153351 18000 # Node ID 2d28f96a309a7ad5d0b9f1358c94e633d6261c2e # Parent 7fb3b742f15fe63290a4caab8c06e3028f1b4223 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd diff -r 7fb3b742f15f -r 2d28f96a309a r_wrapper.sh --- a/r_wrapper.sh Tue Oct 13 12:36:30 2015 -0400 +++ b/r_wrapper.sh Wed Dec 07 18:29:11 2016 -0500 @@ -1,6 +1,6 @@ #!/bin/sh -### Run R providing the R script in $1 as standard input and passing +### 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 @@ -11,7 +11,7 @@ } # Ensure R executable is found -which R > /dev/null || fail "'R' is required by this tool but was not found on path" +which R > /dev/null || fail "'R' is required by this tool but was not found on path" # Extract first argument infile=$1; shift diff -r 7fb3b742f15f -r 2d28f96a309a test-data/testinput2.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/testinput2.tsv Wed Dec 07 18:29:11 2016 -0500 @@ -0,0 +1,82 @@ +numsampled 0.03-F3D0 0.03-F3D1 +1 1 1 +100 41.656 45.056 +200 59.033 61.574 +300 70.564 71.47 +400 78.832 78.473 +500 85.365 83.999 +600 90.809 88.67 +700 95.37 92.661 +800 99.424 96.192 +900 102.93 99.322 +1000 106.109 102.104 +1100 109.093 104.719 +1200 111.779 107.177 +1300 114.358 109.452 +1400 116.659 111.602 +1500 118.767 113.489 +1600 120.752 115.256 +1700 122.691 116.981 +1800 124.511 118.561 +1900 126.265 120.041 +2000 127.967 121.466 +2100 129.51 122.863 +2200 130.973 124.201 +2300 132.418 125.504 +2400 133.783 126.659 +2440 134.324 127.108 +2450 134.432 127.22 +2500 135.037 127.781 +2600 136.268 128.837 +2700 137.479 129.829 +2800 138.638 130.799 +2900 139.759 131.741 +3000 140.851 132.618 +3100 141.941 133.494 +3200 142.993 134.339 +3300 144.002 135.161 +3400 144.999 135.897 +3482 145.788 136.509 +3497 145.931 136.616 +3500 145.967 136.635 +3600 146.838 137.341 +3700 147.726 137.99 +3800 148.541 138.637 +3877 149.223 139.149 +3900 149.396 139.3 +4000 150.177 139.985 +4082 150.853 140.463 +4100 150.991 140.575 +4169 151.478 141.019 +4200 151.704 141.206 +4287 152.323 141.704 +4300 152.429 141.784 +4400 153.157 142.358 +4500 153.884 142.945 +4600 154.56 143.523 +4690 155.146 144 +4698 155.195 NA +4700 155.207 NA +4800 155.864 NA +4900 156.501 NA +5000 157.099 NA +5100 157.699 NA +5200 158.304 NA +5300 158.887 NA +5315 158.968 NA +5400 159.501 NA +5500 160.099 NA +5582 160.613 NA +5600 160.709 NA +5700 161.263 NA +5773 161.67 NA +5800 161.81 NA +5900 162.337 NA +6000 162.853 NA +6100 163.362 NA +6200 163.873 NA +6223 164 NA +6300 NA NA +6400 NA NA +6437 NA NA +6500 NA NA diff -r 7fb3b742f15f -r 2d28f96a309a test-data/testoutput.png Binary file test-data/testoutput.png has changed diff -r 7fb3b742f15f -r 2d28f96a309a xy_plot.xml --- a/xy_plot.xml Tue Oct 13 12:36:30 2015 -0400 +++ b/xy_plot.xml Wed Dec 07 18:29:11 2016 -0500 @@ -1,151 +1,187 @@ - - for multiple series and graph types - - R - - r_wrapper.sh $script_file - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ## 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${i}, yrange ) - #end for - ## Open output PDF file - pdf( "${out_file1}" ) - ## 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() - - - - - - - - - - - - - - - - - - - - - - - -.. 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 - - + + for multiple series and graph types + + R + fontconfig + + r_wrapper.sh $script_file + + + ## 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( "${s.input.file_name}", h=${s.header} ) + x${i} = s${i}[,${s.xcol}] + yrange = 0 + #for $column in str($s.ycol).split(','): + y${i}${column} = s${i}[,${column}] + yrange = range(y${i}${column}, yrange, na.rm=TRUE ) + #end for + xrange = range( x${i}, xrange, na.rm=TRUE ) + #end for + ## Open output PDF file + #if $outftype.value == "pdf" + pdf("outfile.pdf") + #else + "${outftype}"( "outfile.${outftype}" , type="cairo") + #end if + ## Dummy plot for axis / labels + plot( NULL, type="n", xlim=xrange, ylim=yrange, main="${main}", xlab="${xlab}", ylab="${ylab}" ) + ## Plot each series + #for $i, $s in enumerate( $series ) + #if $s.series_type['type'] == "line" + #for $column in str($s.ycol).split(','): + lines( x${i}, y${i}${column}, lty=${s.series_type.lty}, lwd=${s.series_type.lwd}, col=${s.series_type.col} ) + #end for + #elif $s.series_type.type == "points" + #for $column in str($s.ycol).split(','): + points( x${i}, y${i}${column}, pch=${s.series_type.pch}, cex=${s.series_type.cex}, col=${s.series_type.col} ) + #end for + #end if + #end for + ## Close the PDF file + devname = dev.off() + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (outftype == 'pdf') + + + (outftype == 'png') + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. 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 + + +