How to set different color for every gene family using chromoMap?
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9 weeks ago

Hello! I need some help please!!

My issue is, that I want to give a specific color for each gene family, for all the CYP (so CYP1...CYPx), one color for all GST (GST1...GSTx), one color for all the GT (GT1...GTx) and one color for all the ABC (ABC1...ABCx). I tried a lot but nothing worked properly. I would appreciate your help.

I have these txt files: chromosome.txt Chr1 1 781000000 Chr2 1 571000000 Chr3 1 522000000 Chr4 1 443000000 Chr5 1 369000000 Chr6 1 359000000 Chr7 1 351000000 Chr0 1 171000000

annotation.txt CYP1 Chr1 780000000 781000000 GST1 Chr2 3053 3153 CYP2 Chr2 3154 3300 GST2 Chr3 55000 55500 GT1 Chr4 12300 12399 GT2 Chr4 16000 16300 ABC1 Chr6 45000 46000 ABC2 Chr7 54555 56555 GST3 Chr5 1 200

Rscript

getwd()

Read tabular data into R

anno_file <- read.table("annotation.txt", header = FALSE, sep = "", dec = ".")

chr_file <- read.table("chromosome.txt", header = FALSE, sep = "", dec = ".")

head(anno_file)

head(chr_file)

library(chromoMap)

passing data.frames directly instead of files

chromoMap(list(chr_file),list(anno_file))

from the above command I take Rplot.png

ChromoMap(list(chr_file),list(anno_file), labels =T, chr_color = c("black"), anno_col = c ("red"), label_angle = -65, chr_length = 6, chr_width = 7, canvas_width = 800, title = "Metabolic enzymes", title_font_size = 12, top_margin = 25, left_margin = 25)

from the above command I take "metabolic enzymes" plot

Rplot Metabolic enzymes

Thank you very much!

chromoMap family color gene • 130 views
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