gnuplot : recommended version?
Hi, I was trying to use the boxplot tool (Graph/Display Data) from within our local Galaxy instance (just updated yesterday). I faced a couple of issues while trying to generate boxplots. I was wondering which gnuplot version is actually recommended? While working with gnuplot version "4.0 patchlevel 0", one of the error messages was: line 0: undefined variable: tmargin gnuplot> plot '/tools/galaxy/database/files/000/dataset_94.dat' using 1:7:11:12:9 with candlesticks lt 1 lw 1 title 'Quartiles' whiskerbars, '' using 1:8:8:8:8 with candlesticks lt -1 lw 2 title 'Medians', "< python -c \"for xval, yvals in [ ( fields[1 - 1], fields[13 - 1].split( ',' ) ) for fields in [ line.rstrip( '\\n\\r' ).split( '\\t' ) for line in open( '/tools/galaxy/database/files/000/dataset_94.dat' ) if not line.startswith( '#' ) ] if len( fields ) > max( 1 - 1, 13 - 1 ) ]: print '\\n'.join( [ '%s\\t%s' % ( xval, yval ) for yval in yvals if yval ] )\"" using 1:2 with points pt 29 title 'Outliers' ^ line 0: ';' expected this can be overcome this by deleting "tmargin" form the "boxplot.xml" file. The second error message: gnuplot> plot '/tools/galaxy/database/files/000/dataset_94.dat' using 1:7:11:12:9 with candlesticks lt 1 lw 1 title 'Quartiles' whiskerbars, '' using 1:8:8:8:8 with candlesticks lt -1 lw 2 title 'Medians', "< python -c \"for xval, yvals in [ ( fields[1 - 1], fields[13 - 1].split( ',' ) ) for fields in [ line.rstrip( '\\n\\r' ).split( '\\t' ) for line in open( '/tools/galaxy/database/files/000/dataset_94.dat' ) if not line.startswith( '#' ) ] if len( fields ) > max( 1 - 1, 13 - 1 ) ]: print '\\n'.join( [ '%s\\t%s' % ( xval, yval ) for yval in yvals if yval ] )\"" using 1:2 with points pt 29 title 'Outliers' ^ line 0: ';' expected Again, I just removed "whiskerbars" and I got my plot... After getting updated my gnuplot (version 4.4), those issues were solved but there was another one related to the fonts, message: "Could not find/open font when opening font "arial", using internal non-scalable font" This could also be "fixed" by setting explicitly the font in the boxplot.xml (according to what I was just told, arial is proprietary and in some linux systems could represent an issue...): For instance: set term png size ${graph_size} font "/usr/share/fonts/liberation/LiberationSans-Regular.ttf,12" anyway, is there any gnuplot version recommended? Could the boxplot.xml be fixed/adapted to cope with those issues? cheers, Erick
Hi Erick, Thanks for your comments and suggestions with the boxplot tool.
While working with gnuplot version "4.0 patchlevel 0", one of the error messages was:
We are using gnuplot version 'gnuplot 4.2 patchlevel 2' and I have updated the tool's requirements tag to contain this information.
After getting updated my gnuplot (version 4.4), those issues were solved but there was another one related to the fonts, message:
"Could not find/open font when opening font "arial", using internal non-scalable font"
This could also be "fixed" by setting explicitly the font in the boxplot.xml (according to what I was just told, arial is proprietary and in some linux systems could represent an issue...):
For instance:
set term png size ${graph_size} font "/usr/share/fonts/liberation/LiberationSans-Regular.ttf,12"
anyway, is there any gnuplot version recommended? Could the boxplot.xml be fixed/adapted to cope with those issues?
This is a libgd / gnuplot configuration issue. See http://gnuplot.sourceforge.net/faq/faq.html#SECTION00091000000000000000 :
png/jpeg/gif These terminal types use the libgd support library, which searches for fonts in the directories given in the environmental variable GDFONTPATH. Once you get libgd fontpaths sorted out, you will probably want to set a default font for gnuplot. For example: setenv GNUPLOT_DEFAULT_GDFONT verdana
I have made this a non-fatal tool warning in rev 3549:7120c4848270. When the default font does not exist, the boxplot will be produced (using the internal font) and the dataset will be green, but the message will still be presented to the user via the info field. Thanks for using Galaxy, Dan On Mar 19, 2010, at 7:30 AM, Erick Antezana wrote:
Hi,
I was trying to use the boxplot tool (Graph/Display Data) from within our local Galaxy instance (just updated yesterday). I faced a couple of issues while trying to generate boxplots. I was wondering which gnuplot version is actually recommended?
While working with gnuplot version "4.0 patchlevel 0", one of the error messages was:
line 0: undefined variable: tmargin
gnuplot> plot '/tools/galaxy/database/files/000/dataset_94.dat' using 1:7:11:12:9 with candlesticks lt 1 lw 1 title 'Quartiles' whiskerbars, '' using 1:8:8:8:8 with candlesticks lt -1 lw 2 title 'Medians', "< python -c \"for xval, yvals in [ ( fields[1 - 1], fields[13 - 1].split( ',' ) ) for fields in [ line.rstrip( '\\n\\r' ).split( '\\t' ) for line in open( '/tools/galaxy/database/files/000/dataset_94.dat' ) if not line.startswith( '#' ) ] if len( fields ) > max( 1 - 1, 13 - 1 ) ]: print '\\n'.join( [ '%s\\t%s' % ( xval, yval ) for yval in yvals if yval ] )\"" using 1:2 with points pt 29 title 'Outliers'
^ line 0: ';' expected
this can be overcome this by deleting "tmargin" form the "boxplot.xml" file.
The second error message:
gnuplot> plot '/tools/galaxy/database/files/000/dataset_94.dat' using 1:7:11:12:9 with candlesticks lt 1 lw 1 title 'Quartiles' whiskerbars, '' using 1:8:8:8:8 with candlesticks lt -1 lw 2 title 'Medians', "< python -c \"for xval, yvals in [ ( fields[1 - 1], fields[13 - 1].split( ',' ) ) for fields in [ line.rstrip( '\\n\\r' ).split( '\\t' ) for line in open( '/tools/galaxy/database/files/000/dataset_94.dat' ) if not line.startswith( '#' ) ] if len( fields ) > max( 1 - 1, 13 - 1 ) ]: print '\\n'.join( [ '%s\\t%s' % ( xval, yval ) for yval in yvals if yval ] )\"" using 1:2 with points pt 29 title 'Outliers'
^ line 0: ';' expected
Again, I just removed "whiskerbars" and I got my plot...
After getting updated my gnuplot (version 4.4), those issues were solved but there was another one related to the fonts, message:
"Could not find/open font when opening font "arial", using internal non-scalable font"
This could also be "fixed" by setting explicitly the font in the boxplot.xml (according to what I was just told, arial is proprietary and in some linux systems could represent an issue...):
For instance:
set term png size ${graph_size} font "/usr/share/fonts/liberation/LiberationSans-Regular.ttf,12"
anyway, is there any gnuplot version recommended? Could the boxplot.xml be fixed/adapted to cope with those issues?
cheers, Erick _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
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Erick Antezana