re-plotHeatmap using outFileNameMatrix

[kopardev]

Deeptools version 3.4.2
Python version 3.7.5

k=3
plotHeatmap \
--matrixFile regions_of_interest_wrt_iCre_D0.computeMatrix.gz \
--outFileName regions_of_interest_wrt_iCre_D0.heatmap.${k}.testing.pdf \
--outFileSortedRegions regions_of_interest_wrt_iCre_D0.heatmap.${k}.testing.sortedregions.txt \
--outFileNameMatrix regions_of_interest_wrt_iCre_D0.heatmap.${k}.testing.matrix.tab \
--kmeans $k \
--colorMap 'RdBu' \
--whatToShow 'plot, heatmap and colorbar' \
--zMin 0 --zMax 3

The above command runs fine and generates the promised output. I was wondering if it is possible to re-plotHeatmap with the outFileNameMatrix file. This will be convenient if I simply need a new version of the plot with new samplesLable or with a different colorMap.

[dpryan79]

Yes, you can replot using the file from outFileNameMatrix. Just use that as the --matrixFile parameter.

[kopardev]

That does not work for me. I keep getting the following error:

Traceback (most recent call last):
  File "/usr/local/anaconda/bin/plotHeatmap", line 12, in <module>
    main(args)
  File "/usr/local/anaconda/lib/python3.7/site-packages/deeptools/plotHeatmap.py", line 788, in main
    hm.read_matrix_file(matrix_file)
  File "/usr/local/anaconda/lib/python3.7/site-packages/deeptools/heatmapper.py", line 779, in read_matrix_file
    chrom, start, end, name, score, strand = region[0:6]
ValueError: not enough values to unpack (expected 6, got 2)

[LeilyR]

I proposed a solution for your issue. Feel free to use it and see if it works for you. I am not so sure what the initial intention of the authors was in saving the matrix in the format they were saving it, so i would wait a little to hear from them before merging it to develop branch. Otherwise, plotHeatmap from plotHeatmap_output_matrix branch should work for you. Let me know if there was any problem.

[soleilll]

hello, i also have this error.
I tried to use the file from --outFileNameMatrix. I gziped the tab file and e-plotHeatmap with the outFileNameMatrix file, but i still get the same error.
So have you solved this problem?

[JorisBI63]

I have also the same error with plotHeatmap 3.5.0:

Traceback (most recent call last): File "/usr/local/anaconda/bin/plotHeatmap", line 12, in <module> main(args) File "/usr/local/anaconda/lib/python3.7/site-packages/deeptools/plotHeatmap.py", line 788, in main hm.read_matrix_file(matrix_file) File "/usr/local/anaconda/lib/python3.7/site-packages/deeptools/heatmapper.py", line 779, in read_matrix_file chrom, start, end, name, score, strand = region[0:6] ValueError: not enough values to unpack (expected 6, got 2)

I need to re-plot the matrix with other values, is there a solution for this problem ?

Thanks in advance.