Merge pull request #105 from maxplanck-ie/use_matplot_lib_test_to_com…

…pare_images

test images using matplotlib.testing, handle NaNs properly for bigwigs

docs/content/tools/hicPlotTADs.rst

@@ -98,9 +98,15 @@ section as `color`, `title`, etc.
    # of 1000000/500 = 2000 bp
    number of bins = 500
    nans to zeros = True
-   # optional. If type is not specified, then a fill curve is plotted.
+   # options are: line, points, fill. Default is fill
+   # to add the preferred line width or point size use:
+   # type = line:lw where lw (linewidth) is float
+   # similary points:ms sets the point size (markersize (ms) to the given float
    type = line
-   # Default is yes, set to no to turn off the visualization of
+   # type = line:0.5
+   # type = points:0.5
+
+   # Default is yes, set to 'no' to turn off the visualization of
    # text showing the data range (eg. 0 - 100) for the track
    show data range = yes
    # in case it can not be guessed by the file ending

hicPlotTADS_template.ini

@@ -48,8 +48,14 @@ width = 1.5
 # for each bin the average value is taken
 number of bins = 500 
 nans to zeros = True
-# optional. If type is not specified, then a fill curve is plotted.
+# options are: line, points, fill. Default is fill
+# to add the preferred line width or point size use:
+# type = line:lw where lw (linewidth) is float
+# similary points:ms sets the point size (markersize (ms) to the given float
 type = line
+# type = line:0.5
+# type = points:0.5
+
 # optional. Default is yes, set to no to turn off the visualization of data range
 show data range = yes
 #optional in case it can not be guessed by the file ending

hicexplorer/hicPlotTADs.py

@@ -40,8 +40,13 @@
 width = 1.5
 number of bins = 500
 nans to zeros = True
-# optional. If type is not specified, then a fill curve is plotted.
+# options are: line, points, fill. Default is fill
+# to add the preferred line width or point size use:
+# type = line:lw where lw (linewidth) is float
+# similary points:ms sets the point size (markersize (ms) to the given float
 type = line
+# type = line:0.5
+# type = points:0.5
 #optional in case it can not be guessed by the file ending
 file_type = bigwig
 

hicexplorer/test/test_data/README

@@ -10,3 +10,7 @@ hicBuildMatrix -s small_test_R1_unsorted.bam small_test_R2_unsorted.bam -rs DpnI
  --restrictionSequence GATC --danglingSequence GATC \
  --minDistance 150  --maxDistance 1500 -o small_test_rf_matrix.h5 --QCfolder QC_rc
 
+# generate test images
+hicPlotTADs --tracks browser_tracks.ini --region chrX:3000000-3500000 --outFileName master_TADs_plot.png
+hicPlotMatrix --matrix Li_et_al_2015.h5 --region chrX:3000000-3500000 --region2 chrX:3100000-3600000 \
+ --outFileName  master_matrix_plot.png --log1p --clearMaskedBins