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shraddhapai / IdeoViz

Plots data associated with genomic intervals along chromosomal ideogram.
GNU General Public License v2.0
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Colour scheme for ideogram #3

Closed shraddhapai closed 6 years ago

shraddhapai commented 6 years ago

A user writes:

I have a question to ask you while I was trying to plotOnIdeo R library. Would you let me know what is cytoband colors mean? Red color means stain value is acen or stalk?

The answer is: both. Dark red is used for acen and stalk.

Here is the specific R code in plotChromValuePair.R that does the mapping for everything but acen: 

  col[grep("gneg", ideo$gieStain)] <- "gray90"
    col[grep("gpos25", ideo$gieStain)] <- "gray75"
    col[grep("gpos33", ideo$gieStain)] <- "gray66"
    col[grep("gpos50", ideo$gieStain)] <- "gray50"
    col[grep("stalk", ideo$gieStain)] <- "darkred" # repetitive areas
    col[grep("gpos66", ideo$gieStain)] <- "gray33"
    col[grep("gpos75", ideo$gieStain)] <- "gray25"

But "darkred" is also used to mark the centrosome (acen).

Hope this helps, Shraddha