Question: Functional Color Scheme Of Genomediagram Plots
2
gravatar for Zach Powers
9.0 years ago by
Zach Powers340
Zach Powers340 wrote:

I am looking for a way to represent functional annotations of genes on GenomeDiagram plots. I have an annotated multi-genbank file and a making plots of the contigs by making a GenomDiagram plot for each one and then piecing them together with ImageMagick's 'montage' command. (see below) Right now I am coloring the ORFs by defining a GenomeDiagram feature based on a string lookup - here is an example:

> if feature.type == "CDS":  
>             if "glycotransferase" in str(feature.qualifiers['product']):
>                    gd_feature_set.add_feature(feature, color="yellow")

What I would like to do is to take advantage of an already existing color-scheme and be able to color all the ORFs by a functional class. In the GenomeDiagram _Color.py sourcefile I notice that there is a nice color scheme based on Artemis. In this scheme ORFs are colored based on whether they are part of a Primary Metabolism, Secondary Metabolism, Chaperones, Regulators, etc.. I am wondering if there as an easyway to map my genes to this or another color scheme.

thanks, zach cp

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ADD COMMENTlink modified 8.7 years ago by Lars Juhl Jensen11k • written 9.0 years ago by Zach Powers340

I would love to help, but I'm not sure exactly what your question is. Could you try to write your question in one sentence?

ADD REPLYlink written 8.7 years ago by Tommy Carstensen40
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