Heatmap generation fails

[mherold1]

Hi,

I'm using the v.1.11 release, installed in a virtual environment alongisde the python dependencies, using python 2.7.3.

It works until heatmap generation, I get the following error message:

[...]
running heatmap generation
traitar/local/lib/python2.7/site-packages/matplotlib/colorbar.py:789: RuntimeWarning: divide by zero encountered in double_scalars
  automin = (y[2] - y[1]) / clen
traitar/local/lib/python2.7/site-packages/matplotlib/colorbar.py:790: RuntimeWarning: divide by zero encountered in double_scalars
  automax = (y[-2] - y[-3]) / clen
Traceback (most recent call last):
  File "traitar/bin/heatmap.py", line 482, in <module>
    heatmap(matrix, row_header, column_header, primary_pt_models, args.color_f, args.row_method, args.column_method, args.row_metric, args.column_metric,   args.out_f, args.sample_f, secondary_pt_models)
  File "traitar/bin/heatmap.py", line 288, in heatmap
    cb = mpl.colorbar.ColorbarBase(axsl, cmap=cmap_p, norm=norm, spacing='proportional', ticks=bounds, boundaries=bounds)
  File "traitar/local/lib/python2.7/site-packages/matplotlib/colorbar.py", line 323, in __init__
    self.draw_all()
  File "traitar/local/lib/python2.7/site-packages/matplotlib/colorbar.py", line 346, in draw_all
    X, Y = self._mesh()
  File "traitar/local/lib/python2.7/site-packages/matplotlib/colorbar.py", line 814, in _mesh
    y = self._proportional_y()
  File "traitar/local/lib/python2.7/site-packages/matplotlib/colorbar.py", line 789, in _proportional_y
    automin = (y[2] - y[1]) / clen
IndexError: index 2 is out of bounds for axis 0 with size 2
traitar/local/lib/python2.7/site-packages/matplotlib/colorbar.py:789: RuntimeWarning: divide by zero encountered in double_scalars
  automin = (y[2] - y[1]) / clen
traitar/local/lib/python2.7/site-packages/matplotlib/colorbar.py:790: RuntimeWarning: divide by zero encountered in double_scalars
  automax = (y[-2] - y[-3]) / clen
Traceback (most recent call last):
  File "traitar/bin/heatmap.py", line 482, in <module>
    heatmap(matrix, row_header, column_header, primary_pt_models, args.color_f, args.row_method, args.column_method, args.row_metric, args.column_metric,   args.out_f, args.sample_f, secondary_pt_models)
  File "traitar/bin/heatmap.py", line 288, in heatmap
    cb = mpl.colorbar.ColorbarBase(axsl, cmap=cmap_p, norm=norm, spacing='proportional', ticks=bounds, boundaries=bounds)
  File "traitar/local/lib/python2.7/site-packages/matplotlib/colorbar.py", line 323, in __init__
    self.draw_all()
  File "traitar/local/lib/python2.7/site-packages/matplotlib/colorbar.py", line 346, in draw_all
    X, Y = self._mesh()
  File "traitar/local/lib/python2.7/site-packages/matplotlib/colorbar.py", line 814, in _mesh
    y = self._proportional_y()
  File "traitar/local/lib/python2.7/site-packages/matplotlib/colorbar.py", line 789, in _proportional_y
    automin = (y[2] - y[1]) / clen
IndexError: index 2 is out of bounds for axis 0 with size 2
Traceback (most recent call last):
  File "traitar/bin/heatmap.py", line 482, in <module>
    heatmap(matrix, row_header, column_header, primary_pt_models, args.color_f, args.row_method, args.column_method, args.row_metric, args.column_metric,   args.out_f, args.sample_f, secondary_pt_models)
  File "traitar/bin/heatmap.py", line 288, in heatmap
    cb = mpl.colorbar.ColorbarBase(axsl, cmap=cmap_p, norm=norm, spacing='proportional', ticks=bounds, boundaries=bounds)
  File "traitar/local/lib/python2.7/site-packages/matplotlib/colorbar.py", line 323, in __init__
    self.draw_all()
  File "traitar/local/lib/python2.7/site-packages/matplotlib/colorbar.py", line 346, in draw_all
    X, Y = self._mesh()
  File "traitar/local/lib/python2.7/site-packages/matplotlib/colorbar.py", line 814, in _mesh
    y = self._proportional_y()
  File "traitar/local/lib/python2.7/site-packages/matplotlib/colorbar.py", line 789, in _proportional_y
    automin = (y[2] - y[1]) / clen
IndexError: index 2 is out of bounds for axis 0 with size 2

I am using the following command:

traitar phenotype traitar_lao traitar_lao_sub/samples.txt from_genes traitar_lao_sub_OUT/ -c 1

For the test data set heatmap generation works.

Attached a subset of the dataset I'm using (first 4 samples instead of 33), as otherwise the file couldn't be uploaded.
traitar_lao_sub.zip

Is this maybe related to the fact that I only have 1 category in the samples.txt file?

[mherold1]

Is this maybe related to the fact that I only have 1 category in the samples.txt file?

This seemed indeed to be the reason for the above error. I changed categories in the samples.txt file from env1 for all to something specific for each sample and it worked. (unless there are more than 15 categories)

[aweimann]

Thanks a lot for reporting that issue. I will add an additional check of the samples file in the next version of Traitar. In the mean time this walk around should work fine (I will take a look into the > 15 categories problem).