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Question: Pathview color code and gene homolog handling?
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gravatar for devang3110
12 months ago by
devang31100
devang31100 wrote:

Hi!

I'm wondering if anyone has an idea of how Pathwview assigns the colors for gene expression data. For eg, if I am plotting a two column data set (untreated, treated) where for a gene i have log2 fold change values of -2.5 in 'untreated' and +4.5 in 'treated', how exactly does pathview arrive at the colours shown? 

Secondly, if (and this is a common situation) I have multiple gene ids in my dataset with the same E.C number, how does Pathview assign a colour/value to this E.C number in the final figure?

 

thanks!

ADD COMMENTlink modified 12 months ago by Luo Weijun1.4k • written 12 months ago by devang31100
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gravatar for Luo Weijun
12 months ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:
Pathview codes user data (gene expression, metabolite levels etc) in certain range (specified by argument limit) linearly into a continuous color spectrum (specified by arguments low, mid and high). Any value out side the limits will be truncated to the closest limit.The default data limit is (-1, 1), but users can adjust the limits freely based on needs. For example, you may specify limit=c(-3, 3) or even limit=c(-2.5, 4.5) to fit your data. Note that you want to specify informative limits as to best view most (but not necessarily all) of your data. In KEGG graph, a gene node (or E.C number in your case) may represent multiple genes/proteins with similar or redundant functional role. The number of member genes range from 1 up to several tens. They are intentionally put together as a single node on pathway graphs for better clarity and readability. Therefore, we do not split node and mark each member genes separately by default. But rather we visualize the node-wise data by summarize gene-wise data, users may specify the summarization method using node.sum arguement. For more information, check the function documentation: ?pathview
ADD COMMENTlink written 12 months ago by Luo Weijun1.4k
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