Plot fingerprint: return proper nans
#1000
Closed
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
changed iteritmes() in estimateEscaleFactor to its python3 compatible items()
* Fixes for 3.4.2 * disable azure on OSX * Closes deeptools#945 * computeMatricOperation dataRange (deeptools#951) * Added dataRange to computeMatricOperation to return min,max,median and 10th and 90th percentile. * fixed pep8 * more pep8 fix * fixed test_sieve of azure tests * one more fix for test_sieve * imported pysam to test_readFiltering.py * updated hash values for test_sieve * fixed galaxy computeMatrixOperation.xml * More fixes for galaxy wrapper * fixed a little typo in bamCompare (deeptools#967) * save the output matrix of the plotheatmap in a format to be compatible with running plotheatmap on it again (deeptools#968) * Plot profile color map (deeptools#971) * Now colors can be set by user for any heatmap in plotProfile. A bug in tick index for plotting heatmap is also fixed. * added a small description * pep8 fix * added sortUsingSamples and clusterUsingSamples to the galaxy wrapper * [WIP] added auto to plotheatmap deeptools#908 (deeptools#982) * added auto to plotheatmap * fixed lint, added warning message, updated the help for zmin, zmax * galaxy test plotPCA * lower down the delat for potPCA galaxy test * fix deeptools#969 (deeptools#970) * fix deeptools#969 * PEP8 * updated changes.txt * fixed a little bug in parseCommon.py which caused flake8 failure. * [WIP] added auto to plotheatmap deeptools#908 (deeptools#982) * added auto to plotheatmap * fixed lint, added warning message, updated the help for zmin, zmax * galaxy test plotPCA * lower down the delat for potPCA galaxy test * updated version and changes * removed alpha from plotPCA test * removed compare="sim_size" * fixed plotHeatmap.xml by removing size from the the params and adding anitizer for the 2 new params. * upated change.txt * updated the doc html Co-authored-by: Devon Ryan <dpryan79@users.noreply.github.com>
…com/dlaehnemann/deepTools into plot-fingerprint_return-proper-NANs
4 tasks
|
thanks! Can you also merge our dev branch to your branch please? |
|
This should be up to date with your So I think this should be fine. I just fixed one of the test failures, as this was simply an expected testing output that needs to read No clue, what's happening there, and which value should be correct. |
|
Maybe I'll try another clean start from the develop branch. |
|
Closing in favor of #1001 |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Welcome to deepTools GitHub repository! Please check the following regarding
your pull request :
Rebased onto develop branch (compare PR #999 )
This problem came up when parsing the OutputQualityMetrics txt output file downstream when it contains the
NAvalues in columns. To be exact, the conversion tofloat()in the multiqc module throws an error and leads to the respective plot being skipped. The conversion that fails is this line:https://github.com/ewels/MultiQC/blob/9760f7561a56c1295a661471d7447abd085b8020/multiqc/modules/deeptools/plotFingerprint.py#L110
According to the documentation of
float(), this should instead readnanto be parsed correctly. And this is whatprint(numpy.NAN)gives (also see numpy.NAN docs and what is used elsewhere in deeptools (a quick grep on thedeeptools/directory did not give any other results for"NA").