issue with heatmap plotting using kmeans

[Saurabh Pradhan]

Hello everyone,

I am using deeptools to generate heatmap. I have version  deeptools 2.5.3-2-503c71b

installed on my system. I can successfully generate heatmap when i do not use any clustering. But as soon as I use kmean i get following error.

I am following below mentioned steps

1.  computeMatrix reference-point -S W35_SATB1_SJP_subtract.bw W35_SATB1_abcam_subtract.bw -R /home/darwin/senescence/WI38_ChIPseq_new/bwa_aligned/PePr_final_peak_files/DE_RIS_genocode.gtf --referencePoint TSS -a 5000 -b 5000 -out SATB1_OIS_TSS_matrix.mat.gz --missingDataAsZero --skipZeros

2.  plotHeatmap -m SATB1_OIS_TSS_matrix.mat.gz -out SATB1_replicates_OIS_kmeans.svg --heatmapHeight 15 --kmeans 2 --refPointLabel TSS --regionsLabel SATB1_Peaks --dpi 600  --plotFileFormat svg --colorMap YlGnBu  --plotTitle 'SATB1_OIS'

error i am getting is as follows:

WARNING: Group 'cluster_1' is too small for plotting, you might want to remove it. There will likely be an error message from matplotlib regarding this below.

Traceback (most recent call last):

  File "/usr/local/bin/plotHeatmap", line 11, in <module>

    main(args)

  File "/usr/local/lib/python2.7/dist-packages/deeptools/plotHeatmap.py", line 627, in main

    hm.matrix.set_group_labels(args.regionsLabel)

  File "/usr/local/lib/python2.7/dist-packages/deeptools/heatmapper.py", line 1081, in set_group_labels

    raise ValueError("length new labels != length original labels")

ValueError: length new labels != length original labels

I am not able to get an plot after this.

could you please suggest what might be going wrong. 

Thank you in advance,

Saurabh

--

Saurabh J. Pradhan
Laboratory of chromatin biology and epigenetics
Centre of Excellence in Epigenetics,
Indian Institute of Science, Education and Research (IISER)
Pune, India

[Devon Ryan]

You've requested two groups via k-means clustering, so you need two
labels to give to --regionsLabel
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany

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[Saurabh Pradhan]

Great !! Thanks Devon,

It worked well for me. I did not realise it. 

Thanking you with Best wishes

Saurabh