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Pasquali-lab / UMI4Cats

An R package for analyzing UMI-4C chromatin contact data.
https://pasquali-lab.github.io/UMI4Cats/
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Plotting UMIs normalised trend across entire domainogram or visible region #13

Closed minimolecule closed 11 months ago

minimolecule commented 1 year ago

Hi, Thank you for making such a brilliant package to help analyse UMI4C data. This may not be an issue, rather the way I am using the package, so apologies in advance if this is due to my own error.

I would like to ask if there is a way to force plotting the UMI normalised trendline across the entire visible co-ordinates of the plot? I had a look at the plotUMI4C function for additional arguments to help do this but was unable to identify relevant settings. Any advice you may have would be great. I have an example of the plot to this post to help explain what I mean. Best wishes, Sunniyat Rplot-pdgfrbp1-allsil-v-jurkat

mireia-bioinfo commented 11 months ago

Hi Sunniyat,

Currently there is no way to automatically zoom to the region that has a normalized trendline. Nonetheless, you can force the plot to zoom in using the xlim argument in the plotting function, for example: 

plotUMI4C(umi,
    grouping = "condition",
    ylim = c(0, 10),
    xlim = c(149e6, 150e6) # You can edit this to add your zoomed in coordinates
)

Sorry for the late response, I hope this was helpful anyways!

Mireia