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Get unequal plot with same input #604

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jimmy200340 opened this issue Apr 27, 2021 · 3 comments · Fixed by #615
Closed

Get unequal plot with same input #604

jimmy200340 opened this issue Apr 27, 2021 · 3 comments · Fixed by #615
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@jimmy200340
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Hi,
I use the same input to generate scatter plot but with different file type. PDF and SVG loos the same, but PNG seems to have less information. Is this normal?

FE25P20
FE25P20_1.pdf
@tskir
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tskir commented Apr 27, 2021

Hi @jimmy200340, thank you for reporting this. No, it doesn't look like a normal behaviour, could be a bug.

Could you share the CNR and CNS files to reproduce this please? (If you can't share them publicly, on option would be to send them to ktsukanov@ebi.ac.uk and I'll take a look.)

@tskir
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tskir commented Apr 28, 2021

Note to self: files received

tskir added a commit that referenced this issue May 9, 2021
@tskir
Disable snapping to avoid losing short segments in PNG output
65c8ca2 
Fixes #604. As a consequence of default behaviour of
matplotlib.pyplot.plot(), some very short lines/segments can disappear
from rasterised output depending on DPI settings. Explicitly disabling
snapping fixes this.
@tskir tskir mentioned this issue May 9, 2021
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@tskir
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tskir commented May 9, 2021

Oof, it took me some time to investigate. Turns out this is a consequence of default behaviour of matplotlib.pyplot.plot(). I've reported it: matplotlib/matplotlib#20192.

Also submitted a PR to fix this in CNVkit based on advice I received from matplotlib developers: #615.

@jimmy200340 Thank you again for reporting & for sending in the files!

@etal etal closed this as completed in #615 May 11, 2021
etal pushed a commit that referenced this issue May 11, 2021
@tskir @etal
Disable snapping to avoid losing short segments in PNG output
d4145c5 
Fixes #604. As a consequence of default behaviour of
matplotlib.pyplot.plot(), some very short lines/segments can disappear
from rasterised output depending on DPI settings. Explicitly disabling
snapping fixes this.
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Disable snapping to avoid losing short segments in PNG output etal/cnvkit
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@jimmy200340 @tskir