Plot Read Count Over Exons For A Gene
HI all,
I have generated the read count data for my genomic locations using bedtools. I need to plot the read count with all exons belonging to the particular gene in one graph (this way for the the genes with their exons on X axis and read count on Y axis. Does anyone know of any R package /tool to do this. Thanks in advance!
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Hi Were you able to draw the plot. Cn you share the code?
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Varun Gupta
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If you give a more detailed description on the data table you have (e.g. give the output of head -n 5 yourFile.txt) I can help you better.
HI Irsan, Thanks for your post in a similar thread. I used that and the graph looks good. But I would like to have it say gene A segmented into its eons on X axis and the counts on Y axis. The header same as the previous Q. Gene Exon Sample1 Sample 2 Sample 3
Also its whole exon, so its a huge file, can I plot for each gene separately but put them in the same pdf???
Loop over your data frame (probably this can be done efficiently with one of the apply functions) and subset the data frame by gene ID, then make the plot for that gene ID.