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Old 02-17-2015, 05:18 AM   #1
samad
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Location: France

Join Date: Apr 2014
Posts: 2
Default color key KEGG views

Hello,
What's the exact meaning of color spectra in pathview R package?
I used the "pathview" function on a list of gene IDs, everything is ok but i can't interpret the colors in the resulted graph.

in the function help, i have this :
low, mid, high each:
is a list of two colors with "gene" and "cpd" as the names. This argument
specifies the color spectra to code gene.data and cpd.data. When data are 1
directional (TRUE value in both.dirs), only mid and high are used to specify the
color spectra. Default spectra (low-mid-high) "green"-"gray"-"red" and "blue"-
"gray"-"yellow" are used for gene.data and cpd.data respectively. The values for
’low, mid, high’ can be given as color names (’red’), plot color index (2=red),
and HTML-style RGB, ("\#FF0000"=red)


link:
http://bioconductor.org/packages/rel...n/pathview.pdf

just wanted to know what does it means when i have "high" (red color) in my graph
sorry if it seems to be stupid question for some of you

cheers
Samad

Last edited by samad; 02-17-2015 at 05:22 AM.
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Old 02-22-2015, 06:39 PM   #2
bigmw
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Posts: 123
Default

Data values are visualized as pseudo colors on pathway graphs. There is usually 1 or 2 color keys (spectra) to show you the mapping between colors and values. Colors in this spectrum can be specified by the users. Arguments-low, mid, high, are used to specify the colors used for lowest, middle and highest data values. If you look at the color keys on the top right corner of the example graphs on the page below (or in the tutorial), you will see it:
http://pathview.r-forge.r-project.org/

BTW, you may want to post your question on the bioinformatics forum instead of general forum next time:
http://seqanswers.com/forums/forumdisplay.php?f=18
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