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plotting bedgraph data for all chromosome at once #139
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Hi @nirvana693 I'm not sure I see what the problem is, so I'll try my best to guess it. Please correct me if I'm wrong. If you are able to plot for a single chromosome, the only thing you need to do to plot the whole genome is changing Hope this helps. And if this was not exactly what you were asking, fell free to reopen the issue :) Bernat |
hi @bernatgel, Thank you for the quick response. Approach1: As shown in my 1st post, when I draw chromosome wise (telomere_plot.R), results are as expected.
as a result of ymax from the whole dataset (in my dataset chr15), data in many chromosomes are not clearly visible. Approach3: So, I tried plotting karyotype outside the loop and process chromosome wise inside the loop as follows:
plot generated without any error/warnings but it appears that chomosome wise data is not rendered correctly. I am trying to plot number of telomere motifs from a assembled genome on chm13. Any suggestions on better representation would be helpful. |
Hi @nirvana693 Thanks for the report and the attached files! I'll take a look at it and try to find out what's going on. I won't be able to take a look at it at least until next Wednesday, though. If you have any other advance in the meantime, please let me know Bernat. |
Hi @bernatgel |
@bernatgel Approach 3 works perfectly if I add the Thank you. |
Thanks for the updates! This is a strange behaviour. I'll take a look at it! |
Hi @bernatgel
Thank you for the awesome tool.
I have a bedgraph data containing genomic window and motif count
I can successfully draw the data using kpBars for each chromosome
![image](https://user-images.githubusercontent.com/45812941/236386099-02e989f2-f2fd-4d91-9a09-4d24fc856e42.png)
But how do I do it for all chromosomes at once in single image? I checked this biostar thread , example given is for single chromosome.
any help would be appreciated. Thank you
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