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ncbi / BAMscale

BAMscale is a one-step tool for either 1) quantifying and normalizing the coverage of peaks or 2) generated scaled BigWig files for easy visualization of commonly used DNA-seq capture based methods.
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k-means error #16

Closed beroult closed 3 years ago

beroult commented 3 years ago

Hello,

When I try to do k-means clustering, I receive an error below. As I searched, this is because of NAs present in the data frame. I m not sure how to omit NAs from peakds data. Thanks in advance for your help.

peakds = PrepareDataForPlotting(peakds) Error in do_one(nmeth) : NA/NaN/Inf in foreign function call (arg 1) Called from: do_one(nmeth)

pongorlorinc commented 3 years ago

Hi Beroult,

Are you using the plotting script in R?

I will have an update for it soon, with a lot of improvements (next 1-2 weeks).

Let me know what other errors you find, to try and smooth them out!

Thank you, Lorinc

beroult commented 3 years ago

Hi Lorinc,

I manage to find the NAs and omitted with the code below.

is.na(peakds$peak_quants) peakds$peak_quants <- na.omit(peakds$peak_quants) peakds$peak_quants

But I encountered other issues that I can share. One is the heatmap clustering output. I tried to find out if my 3 stages(st0, st1,st2) were differing in accessibility when treated with VPA (see the plot below). I think they all look the same. Also, I cant plot for the Application for Plotting Peak-Density Figures. I get such a figure. Thanks for the help.

Heatmap_plot.pdf

Screen Shot 2021-05-13 at 11 15 07 AM
pongorlorinc commented 3 years ago

Hi Beroult,

Sorry for not getting back earlier.

The XY plot you are showing seems to be zoomed out a bit too much (too many outlier peaks with strong signal). Could you try decreasing the limit at the "Axis Limit Slider"? Based on the heatmap, I would try going town to maybe 5 in normalized signal.

Best wishes, Lorinc

beroult commented 3 years ago

Hi Lorinc,

I decreased the axis limit slider and still I dont see a density plot. Besides, I coul not find the option to make the normalized signal to set for 5. It would be great if you share the code for setting this. And when I run the codes again even though I did not change anything, my heatmap plot changed a bit. Thanks very much for the help. Looking forward to hear from you.

Kind regards,

Beri [image: Screen Shot 2021-05-19 at 2.26.27 PM.png]

pongorlorinc @.***>, 16 May 2021 Paz, 00:01 tarihinde şunu yazdı:

Hi Beroult,

Sorry for not getting back earlier.

The XY plot you are showing seems to be zoomed out a bit too much (too many outlier peaks with strong signal). Could you try decreasing the limit at the "Axis Limit Slider"? Based on the heatmap, I would try going town to maybe 5 in normalized signal.

Best wishes, Lorinc

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-- Berivan Temiz

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Wilson Laboratory

Department of Anatomy | School of Biomedical Sciences | University of Otago Te Tari Kikokiko | Te Kura Mātai Rongoā-Koiora | Te Whare Wānanga o Otāgo

pongorlorinc commented 3 years ago

Hi Beroult,

I uploaded a new version for the density under the "R/BAMscale_peak_density_version2" folder. Hopefully this will help better change axis limits.

Let me know, if it helped!

Best wishes, Lorinc