Need help with heatmaps in QIIME
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Entering edit mode
5.2 years ago

Hi all

I am trying to create a heat map in qiime for a sample.

When I use the command make_otu_heatmap.py -i otu_table.biom -m S1.txt -t rep_set.tre -o h1 a heatmap is generated but there is no differentiation.

Then I used make_otu_heatmap.py -i otu_table.biom -m S1.txt -t rep_set.tre -c Description -o h1 and now no heatmap is created and a error appears.

saikiran@saiki:~/new ngs$ make_otu_heatmap.py -i otu_table.biom -m S1.txt -t rep_set.tre -c Description -o h1 Traceback (most recent call last): File "/usr/local/bin/make_otu_heatmap.py", line 254, in <module> main() File "/usr/local/bin/make_otu_heatmap.py", line 200, in main category_labels) File "/usr/local/lib/python2.7/dist-packages/qiime/make_otu_heatmap.py", line 69, in get_order_from_categories label_ix_ix = get_clusters(data, axis='column') File "/usr/local/lib/python2.7/dist-packages/qiime/make_otu_heatmap.py", line 138, in get_clusters linkage_matrix = linkage(row_dissims.condensed_form(), method='average') File "/usr/local/lib/python2.7/dist-packages/scipy/cluster/hierarchy.py", line 678, in linkage n = int(distance.num_obs_y(y)) File "/usr/local/lib/python2.7/dist-packages/scipy/spatial/distance.py", line 1812, in num_obs_y raise ValueError("The number of observations cannot be determined on " ValueError: The number of observations cannot be determined on an empty distance matrix.

Please help me create a proper heatmap.

Kiran

Heatmaps qiime • 1.9k views
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Entering edit mode
5.2 years ago

heatmap

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