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issues related to plotCorrelation #1159

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ccmeth opened this issue Sep 15, 2022 · 5 comments
Closed

issues related to plotCorrelation #1159

ccmeth opened this issue Sep 15, 2022 · 5 comments

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@ccmeth
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ccmeth commented Sep 15, 2022

Hi,
Thanks a lot for providing such a powerful tool for data analysis. However, after multibigwigsummary and plotcorrelation, I noticed that the figures generated was a little strange. The line does not correspond to the sample accurately. Could you please provide any suggestions?
deeptools version: 3.5.1
python version: 3.8.10

ATAC_heatmap_SpearmanCorr_bw
@adRn-s
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adRn-s commented Sep 15, 2022

Please clarify, which line do you mean? The bordeaux 'tree' on the left is a hierarchical clustering based on this Spearman correlation values.

@ccmeth
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ccmeth commented Sep 15, 2022

Please clarify, which line do you mean? The bordeaux 'tree' on the left is a hierarchical clustering based on this Spearman correlation values.

Sorry, the line means the "tree line", which does not always point to the center.

@adRn-s
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adRn-s commented Sep 15, 2022

Ah, now I see it. Thanks! I believe I have found the source of the problem... we'll let you know as soon as we push a fix.

@ccmeth
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ccmeth commented Sep 15, 2022

Ah, now I see it. Thanks! I believe I have found the source of the problem... we'll let you know as soon as we push a fix.

Thanks for your timely reply!

@adRn-s adRn-s closed this as completed in d2fa070 Sep 15, 2022
@adRn-s
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adRn-s commented Sep 15, 2022

the latest code on develop branch has this update in place.

adRn-s added a commit that referenced this issue Sep 15, 2022
@adRn-s
fix #1159
eddb56e
adRn-s added a commit that referenced this issue Jan 5, 2023
@lldelisle @adRn-s @LeilyR
Bigwig average (#1169)
8d9be32 
* Fixes #1159

* Revert "dendogram of plotCorrelation now matches each cell correctly"

* add bigwigAverage

* linting

* remove forgotten prints

* make bigwigAverage executable

* fix galaxy tests

Co-authored-by: A.s <62971995+adRn-s@users.noreply.github.com>
Co-authored-by: LeilyR <25766687+LeilyR@users.noreply.github.com>
adRn-s added a commit that referenced this issue Feb 3, 2023
@adRn-s @gallardoalba
@bgruening @LeilyR @lldelisle
Develop (#1185)
3005380 
* Fix label options

* add pool

* trigger test

* new azure syntax?

* run also on PR

* fix #1159

* fixes #1172

* Addressing #1181

* Bigwig average (#1169)

* Fixes #1159

* Revert "dendogram of plotCorrelation now matches each cell correctly"

* add bigwigAverage

* linting

* remove forgotten prints

* make bigwigAverage executable

* fix galaxy tests

Co-authored-by: A.s <62971995+adRn-s@users.noreply.github.com>
Co-authored-by: LeilyR <25766687+LeilyR@users.noreply.github.com>

* Addresses #1183

* Fix galaxy tests (#1186)

* upload artifact

* allow 1 or 2 lines diff for bowtie2 program

* change github action to get artifacts

* fix plotPCA

* try to fix old samtools installed

* add forgotten channels

---------

Co-authored-by: Cristóbal Gallardo <gallardo@informatik.uni-freiburg.de>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: LeilyR <25766687+LeilyR@users.noreply.github.com>
Co-authored-by: Lucille Delisle <lucille.delisle@epfl.ch>
Co-authored-by: adRn-s <salatino@omics.dev>
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@ccmeth @adRn-s