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RegulatoryGenomicsGroup / chicdiff

A differential caller for capture Hi-C data
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Plotting gene names along with bait IDs in plotDiffBaits #22

Open RomeroMatt opened 5 months ago

RomeroMatt commented 5 months ago

Hello, Thanks for this great tool! I am plotting various baits and I noticed in the vignette the plots have gene names, whereas none of the plots I have generated contain gene names. I looked at the help page for plotDIffBaits(), but can't find any info on this. Would this be something the user has to add post-hoc?

Thanks again! -Matt

mspivakov commented 5 months ago

Happy to hear you like it! In principle this should work automatically as plotBaitNames=TRUE by default. Could it be that gene names aren't recorded in your baitName column?

RomeroMatt commented 5 months ago

That must be the case. When I run the test code I see the names, but my data comes up differently. I've attached the two pics. Do you know how I would add the gene names to the column? test_diffbaitPlot shelton_fetal_diffbaitPlot

RomeroMatt commented 5 months ago

I think I see where things might be able to be fixed. Here's my baitmap: chr1 11160 17953 2 1 chr1 17954 23311 3 2 chr1 29507 34831 5 3 chr1 60526 65662 11 4 chr1 65663 70688 12 5 chr1 132426 137846 25 6 chr1 153626 158654 29 7 chr1 158655 163905 30 8 chr1 184432 189972 35 9 chr1 446674 451915 67 10

It looks like the first three are coordinates, followed by the BaitID in column 4 and instead of a gene name in the fifth column, it's just numbered 1-(...). This baitmap was generated from Arima as I am using their kit. Maybe I can match the coordinates of the baitmap with a gene coordinate bed file and replace column five with gene name? Or is the fifth column used in the analysis?

Thanks!

mspivakov commented 5 months ago

Yeah, the last column would normally contain bait annotations.

On Thu, 4 Apr 2024, 00:41 RomeroMatt, @.***> wrote:

I think I see where things might be able to be fixed. Here's my baitmap: chr1 11160 17953 2 1 chr1 17954 23311 3 2 chr1 29507 34831 5 3 chr1 60526 65662 11 4 chr1 65663 70688 12 5 chr1 132426 137846 25 6 chr1 153626 158654 29 7 chr1 158655 163905 30 8 chr1 184432 189972 35 9 chr1 446674 451915 67 10

It looks like the first three are coordinates, followed by the BaitID in column 4 and instead of a gene name in the fifth column, it's just numbered 1-(...). This baitmap was generated from Arima as I am using their kit. Maybe I can match the coordinates of the baitmap with a gene coordinate bed file and replace column five with gene name? Or is the fifth column used in the analysis?

Thanks!

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