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Merge pull request #163 from deeptools/master-patch
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Master patch
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@joachimwolff
joachimwolff authored Dec 28, 2017
2 parents ee161a2 + 21b22e0 commit 8e5298c
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Showing 8 changed files with 50 additions and 31 deletions.
2 changes: 1 addition & 1 deletion docs/content/installation.rst
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Expand Up @@ -10,7 +10,7 @@ Requirements
* Python 2.7 or 3.6
* numpy >= 1.12.1
* scipy >= 0.19.0
* matplotlib >= 2.0.0
* matplotlib == 2.1.1
* pysam >= 0.11.2
* intervaltree >= 2.1.0
* biopython >= 1.68
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17 changes: 16 additions & 1 deletion hicexplorer/hicCorrectMatrix.py
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Expand Up @@ -333,8 +333,17 @@ def value_to_mad(self, value):
return the mad value for a given value
based on the data
"""

log.debug("self.median: {}".format(self.median))
diff = value - self.median
log.debug("diff: {}".format(diff))
log.debug("self.med_abs_deviation: {}".format(self.med_abs_deviation))
log.debug("self.mad_b_value: {}".format(self.mad_b_value))
log.debug("all together: {}".format(self.mad_b_value * diff / self.med_abs_deviation))
# workaround for 'Axis limits cannot be NaN or Inf' bug in version 2.1.1
# prevent dividing by 0!!!
if self.med_abs_deviation == 0.0:
return self.mad_b_value * diff

return self.mad_b_value * diff / self.med_abs_deviation

def mad_to_value(self, mad):
Expand Down Expand Up @@ -391,6 +400,12 @@ def plot_histogram(row_sum_values, mad_values, ax1, title=None):
# update second axis values by mapping the min max
# of the main axis to the translated values
# into modified z score.

# workaround for 'Axis limits cannot be NaN or Inf' bug in version 2.1.1
log.debug("ax1.get_xlim(): {}".format(ax1.get_xlim()))
log.debug("np.array(ax1.get_xlim()): {}".format(np.array(ax1.get_xlim())))
log.debug("mad_values.value_to_mad(np.array(ax1.get_xlim())): {}".format(mad_values.value_to_mad(np.array(ax1.get_xlim()))))

ax2.set_xlim(mad_values.value_to_mad(np.array(ax1.get_xlim())))

# get first local mininum value
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Binary file added hicexplorer/test/test_data/hicMergeMatrixBins/result.h5
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Binary file modified hicexplorer/test/test_data/hicPlotDistVsCounts/dist_vs_counts.png
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11 changes: 7 additions & 4 deletions hicexplorer/test/test_hicPlotDistVsCounts.py
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Expand Up @@ -4,7 +4,6 @@

import matplotlib as mpl
mpl.use('agg')
from matplotlib.testing.compare import compare_images
import os.path


Expand All @@ -15,10 +14,14 @@ def test_plot():

outfile = NamedTemporaryFile(suffix='.png', prefix='plotFile', delete=False)
matrix = ROOT + 'small_test_matrix_50kb_res.h5'
args = "--matrices {} --plotFile {}".format(matrix, outfile.name).split()
args = "--matrices {} --plotFile {} --plotsize 6 4".format(matrix, outfile.name).split()
hicPlotDistVsCounts.main(args)

res = compare_images(ROOT + 'hicPlotDistVsCounts/dist_vs_counts.png', outfile.name, tol=40)
assert res is None, res
# don't using matplotlib compare images not anymore
# because matplotlib is, depending on version, implementation or context,
# slightly different images
size_new = os.path.getsize(outfile.name)
size_reference = os.path.getsize(ROOT + 'hicPlotDistVsCounts/dist_vs_counts.png',)
assert abs(size_new - size_reference) < 3000

os.remove(outfile.name)
47 changes: 24 additions & 23 deletions hicexplorer/test/test_hicPlotMatrix.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,15 +9,16 @@
mem = virtual_memory()
memory = mem.total / 2**30
import hicexplorer.hicPlotMatrix
tolerance = 13 # default matplotlib pixed difference tolerance
tolerance = 60 # default matplotlib pixed difference tolerance
ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"

# memory in GB the test computer needs to have to run the test case
LOW_MEMORY = 2
MID_MEMORY = 7
HIGH_MEMORY = 20
HIGH_MEMORY = 200

REMOVE_OUTPUT = True
# DIFF = 60


@pytest.mark.skipif(MID_MEMORY > memory,
Expand Down Expand Up @@ -137,7 +138,7 @@ def test_hicPlotMatrix_cool_region1_region2():
args = "--matrix {0}/Li_et_al_2015.cool --region chrX:3000000-3500000 --region2 chrX:3100000-3600000 " \
"--outFileName {1} ".format(ROOT, outfile.name).split()
hicexplorer.hicPlotMatrix.main(args)
res = compare_images(ROOT + "hicPlotMatrix" + '/Li_chrX30-35-chrX31-36_cool.png', outfile.name, tol=40)
res = compare_images(ROOT + "hicPlotMatrix" + '/Li_chrX30-35-chrX31-36_cool.png', outfile.name, tol=tolerance)
assert res is None, res
if REMOVE_OUTPUT:
os.remove(outfile.name)
Expand All @@ -152,7 +153,7 @@ def test_hicPlotMatrix_cool_region1():
args = "--matrix {0}/Li_et_al_2015.cool --region X:3000000-3500000 " \
"--outFileName {1} ".format(ROOT, outfile.name).split()
hicexplorer.hicPlotMatrix.main(args)
res = compare_images(ROOT + "hicPlotMatrix" + '/Li_chrX30-35_cool.png', outfile.name, tol=40)
res = compare_images(ROOT + "hicPlotMatrix" + '/Li_chrX30-35_cool.png', outfile.name, tol=tolerance)
assert res is None, res
if REMOVE_OUTPUT:
os.remove(outfile.name)
Expand All @@ -167,7 +168,7 @@ def test_hicPlotMatrix_cool_log1p():
args = "--matrix {0}/Li_et_al_2015.cool --log1p " \
"--outFileName {1} ".format(ROOT, outfile.name).split()
hicexplorer.hicPlotMatrix.main(args)
res = compare_images(ROOT + "hicPlotMatrix" + '/Li_cool_log1p.png', outfile.name, tol=40)
res = compare_images(ROOT + "hicPlotMatrix" + '/Li_cool_log1p.png', outfile.name, tol=tolerance)
assert res is None, res
if REMOVE_OUTPUT:
os.remove(outfile.name)
Expand All @@ -182,7 +183,7 @@ def test_hicPlotMatrix_cool_log():
args = "--matrix {0}/Li_et_al_2015.cool --log " \
"--outFileName {1} ".format(ROOT, outfile.name).split()
hicexplorer.hicPlotMatrix.main(args)
res = compare_images(ROOT + "hicPlotMatrix" + '/Li_cool_log.png', outfile.name, tol=40)
res = compare_images(ROOT + "hicPlotMatrix" + '/Li_cool_log.png', outfile.name, tol=tolerance)
assert res is None, res
if REMOVE_OUTPUT:
os.remove(outfile.name)
Expand All @@ -197,7 +198,7 @@ def test_hicPlotMatrix_cool_full():
args = "--matrix {0}/Li_et_al_2015.cool " \
"--outFileName {1} ".format(ROOT, outfile.name).split()
hicexplorer.hicPlotMatrix.main(args)
res = compare_images(ROOT + "hicPlotMatrix" + '/Li_cool.png', outfile.name, tol=40)
res = compare_images(ROOT + "hicPlotMatrix" + '/Li_cool.png', outfile.name, tol=tolerance)
assert res is None, res
if REMOVE_OUTPUT:
os.remove(outfile.name)
Expand All @@ -212,7 +213,7 @@ def test_hicPlotMatrix_h5_log1p():
args = "--matrix {0}/Li_et_al_2015.h5 --log1p " \
"--outFileName {1} ".format(ROOT, outfile.name).split()
hicexplorer.hicPlotMatrix.main(args)
res = compare_images(ROOT + "hicPlotMatrix" + '/Li_h5_log1p.png', outfile.name, tol=40)
res = compare_images(ROOT + "hicPlotMatrix" + '/Li_h5_log1p.png', outfile.name, tol=tolerance)
assert res is None, res
if REMOVE_OUTPUT:
os.remove(outfile.name)
Expand All @@ -227,7 +228,7 @@ def test_hicPlotMatrix_h5_log():
args = "--matrix {0}/Li_et_al_2015.h5 --log " \
"--outFileName {1} ".format(ROOT, outfile.name).split()
hicexplorer.hicPlotMatrix.main(args)
res = compare_images(ROOT + "hicPlotMatrix" + '/Li_h5_log.png', outfile.name, tol=40)
res = compare_images(ROOT + "hicPlotMatrix" + '/Li_h5_log.png', outfile.name, tol=tolerance)
assert res is None, res
if REMOVE_OUTPUT:
os.remove(outfile.name)
Expand All @@ -242,7 +243,7 @@ def test_hicPlotMatrix_h5_full():
args = "--matrix {0}/Li_et_al_2015.h5 " \
"--outFileName {1} ".format(ROOT, outfile.name).split()
hicexplorer.hicPlotMatrix.main(args)
res = compare_images(ROOT + "hicPlotMatrix" + '/Li_h5.png', outfile.name, tol=40)
res = compare_images(ROOT + "hicPlotMatrix" + '/Li_h5.png', outfile.name, tol=tolerance)
assert res is None, res
if REMOVE_OUTPUT:
os.remove(outfile.name)
Expand All @@ -257,7 +258,7 @@ def test_hicPlotMatrix_cool_log_region1_region2():
args = "--matrix {0}/Li_et_al_2015.cool --region chrX:3000000-3500000 --region2 chrX:3100000-3600000 " \
"--outFileName {1} --log ".format(ROOT, outfile.name).split()
hicexplorer.hicPlotMatrix.main(args)
res = compare_images(ROOT + "hicPlotMatrix" + '/Li_chrX30-35-chrX31-36_cool_log.png', outfile.name, tol=40)
res = compare_images(ROOT + "hicPlotMatrix" + '/Li_chrX30-35-chrX31-36_cool_log.png', outfile.name, tol=tolerance)
assert res is None, res
if REMOVE_OUTPUT:
os.remove(outfile.name)
Expand All @@ -272,7 +273,7 @@ def test_hicPlotMatrix_cool_log_region1_region2_without_cool_suffix():
args = "--matrix {0}/Li_et_al_2015 --region chrX:3000000-3500000 --region2 chrX:3100000-3600000 " \
"--outFileName {1} --log ".format(ROOT, outfile.name).split()
hicexplorer.hicPlotMatrix.main(args)
res = compare_images(ROOT + "hicPlotMatrix" + '/Li_chrX30-35-chrX31-36_cool_log.png', outfile.name, tol=40)
res = compare_images(ROOT + "hicPlotMatrix" + '/Li_chrX30-35-chrX31-36_cool_log.png', outfile.name, tol=tolerance)
assert res is None, res
if REMOVE_OUTPUT:
os.remove(outfile.name)
Expand All @@ -287,7 +288,7 @@ def test_hicPlotMatrix_cool_log1p_region1_region2():
args = "--matrix {0}/Li_et_al_2015.cool --region chrX:3000000-3500000 --region2 chrX:3100000-3600000 " \
"--outFileName {1} --log1p ".format(ROOT, outfile.name).split()
hicexplorer.hicPlotMatrix.main(args)
res = compare_images(ROOT + "hicPlotMatrix" + '/Li_chrX30-35-chrX31-36_cool_log1p.png', outfile.name, tol=40)
res = compare_images(ROOT + "hicPlotMatrix" + '/Li_chrX30-35-chrX31-36_cool_log1p.png', outfile.name, tol=tolerance)
assert res is None, res
if REMOVE_OUTPUT:
os.remove(outfile.name)
Expand All @@ -302,7 +303,7 @@ def test_hicPlotMatrix_perChr():
args = "--matrix {0}/small_test_matrix_50kb_res.h5 --perChr " \
"--outFileName {1} ".format(ROOT, outfile.name).split()
hicexplorer.hicPlotMatrix.main(args)
res = compare_images(ROOT + "hicPlotMatrix" + '/small_test_matrix_50kb_res_perChr.png', outfile.name, tol=40)
res = compare_images(ROOT + "hicPlotMatrix" + '/small_test_matrix_50kb_res_perChr.png', outfile.name, tol=tolerance)
assert res is None, res
if REMOVE_OUTPUT:
os.remove(outfile.name)
Expand All @@ -317,7 +318,7 @@ def test_hicPlotMatrix_perChr_without_h5_suffix():
args = "--matrix {0}/small_test_matrix_50kb_res --perChr " \
"--outFileName {1} ".format(ROOT, outfile.name).split()
hicexplorer.hicPlotMatrix.main(args)
res = compare_images(ROOT + "hicPlotMatrix" + '/small_test_matrix_50kb_res_perChr.png', outfile.name, tol=40)
res = compare_images(ROOT + "hicPlotMatrix" + '/small_test_matrix_50kb_res_perChr.png', outfile.name, tol=tolerance)
assert res is None, res
if REMOVE_OUTPUT:
os.remove(outfile.name)
Expand All @@ -332,7 +333,7 @@ def test_hicPlotMatrix_cool_perChr_log():
args = "--matrix {0}/small_test_matrix_50kb_res.h5 --perChr " \
"--outFileName {1} --log ".format(ROOT, outfile.name).split()
hicexplorer.hicPlotMatrix.main(args)
res = compare_images(ROOT + "hicPlotMatrix" + '/small_test_matrix_50kb_res_perChr_log.png', outfile.name, tol=40)
res = compare_images(ROOT + "hicPlotMatrix" + '/small_test_matrix_50kb_res_perChr_log.png', outfile.name, tol=tolerance)
assert res is None, res
if REMOVE_OUTPUT:
os.remove(outfile.name)
Expand All @@ -347,7 +348,7 @@ def test_hicPlotMatrix_cool_perChr_log1p_chromosomeOrder():
args = "--matrix {0}/small_test_matrix_50kb_res.h5 --perChr " \
"--outFileName {1} --log1p --chromosomeOrder chr2L chr3L chr3R chr2R".format(ROOT, outfile.name).split()
hicexplorer.hicPlotMatrix.main(args)
res = compare_images(ROOT + "hicPlotMatrix" + '/small_test_matrix_perChr_log1p_chromosomeOrder.png', outfile.name, tol=40)
res = compare_images(ROOT + "hicPlotMatrix" + '/small_test_matrix_perChr_log1p_chromosomeOrder.png', outfile.name, tol=tolerance)
assert res is None, res
if REMOVE_OUTPUT:
os.remove(outfile.name)
Expand All @@ -362,7 +363,7 @@ def test_hicPlotMatrix_perChr_pca1_bigwig():
args = "--matrix {0}/hicTransform/pearson_small_50kb.h5 --perChr " \
"--outFileName {1} --pca {2}".format(ROOT, outfile.name, ROOT + "hicPCA/pca1.bw").split()
hicexplorer.hicPlotMatrix.main(args)
res = compare_images(ROOT + "hicPlotMatrix" + '/small_matrix_50kb_pearson_pca1_plot.png', outfile.name, tol=40)
res = compare_images(ROOT + "hicPlotMatrix" + '/small_matrix_50kb_pearson_pca1_plot.png', outfile.name, tol=tolerance)
assert res is None, res
if REMOVE_OUTPUT:
os.remove(outfile.name)
Expand All @@ -377,7 +378,7 @@ def test_hicPlotMatrix_perChr_pca2_bedgraph():
args = "--matrix {0}/hicTransform/pearson_small_50kb.h5 --perChr " \
"--outFileName {1} --pca {2}".format(ROOT, outfile.name, ROOT + "hicPCA/pca2.bedgraph").split()
hicexplorer.hicPlotMatrix.main(args)
res = compare_images(ROOT + "hicPlotMatrix" + '/small_matrix_50kb_pearson_pca2_plot.png', outfile.name, tol=40)
res = compare_images(ROOT + "hicPlotMatrix" + '/small_matrix_50kb_pearson_pca2_plot.png', outfile.name, tol=tolerance)
assert res is None, res
if REMOVE_OUTPUT:
os.remove(outfile.name)
Expand All @@ -392,7 +393,7 @@ def test_hicPlotMatrix_region_pca1_colormap_bedgraph():
args = "--matrix {0}/hicTransform/pearson_small_50kb.h5 --region chr2L " \
"--outFileName {1} --pca {2} --colorMap hot".format(ROOT, outfile.name, ROOT + "hicPCA/pca1.bedgraph").split()
hicexplorer.hicPlotMatrix.main(args)
res = compare_images(ROOT + "hicPlotMatrix" + '/small_test_50kb_pearson_pca1_plot_region__colormap_hot_chr2L.png', outfile.name, tol=40)
res = compare_images(ROOT + "hicPlotMatrix" + '/small_test_50kb_pearson_pca1_plot_region__colormap_hot_chr2L.png', outfile.name, tol=tolerance)
assert res is None, res
if REMOVE_OUTPUT:
os.remove(outfile.name)
Expand All @@ -407,7 +408,7 @@ def test_hicPlotMatrix_region_start_end_pca1_colormap_bedgraph():
args = "--matrix {0}/hicTransform/pearson_small_50kb.h5 --region chr2L:15000000-20000000 " \
"--outFileName {1} --pca {2} --colorMap hot".format(ROOT, outfile.name, ROOT + "hicPCA/pca1.bedgraph").split()
hicexplorer.hicPlotMatrix.main(args)
res = compare_images(ROOT + "hicPlotMatrix" + '/small_test_50kb_pearson_pca1_plot_region__colormap_hot_chr2L_15mb-20mb.png', outfile.name, tol=40)
res = compare_images(ROOT + "hicPlotMatrix" + '/small_test_50kb_pearson_pca1_plot_region__colormap_hot_chr2L_15mb-20mb.png', outfile.name, tol=tolerance)
assert res is None, res
if REMOVE_OUTPUT:
os.remove(outfile.name)
Expand All @@ -422,7 +423,7 @@ def test_hicPlotMatrix_region_pca1_colormap_bigwig():
args = "--matrix {0}/hicTransform/pearson_small_50kb.h5 --region chr2L " \
"--outFileName {1} --pca {2} --colorMap hot".format(ROOT, outfile.name, ROOT + "hicPCA/pca1.bw").split()
hicexplorer.hicPlotMatrix.main(args)
res = compare_images(ROOT + "hicPlotMatrix" + '/small_test_50kb_pearson_pca1_plot_region__colormap_hot_chr2L_bw.png', outfile.name, tol=40)
res = compare_images(ROOT + "hicPlotMatrix" + '/small_test_50kb_pearson_pca1_plot_region__colormap_hot_chr2L_bw.png', outfile.name, tol=tolerance)
assert res is None, res
if REMOVE_OUTPUT:
os.remove(outfile.name)
Expand All @@ -437,7 +438,7 @@ def test_hicPlotMatrix_region_start_end_pca1_colormap_bigwig():
args = "--matrix {0}/hicTransform/pearson_small_50kb.h5 --region chr2L:15000000-20000000 " \
"--outFileName {1} --pca {2} --colorMap hot".format(ROOT, outfile.name, ROOT + "hicPCA/pca1.bw").split()
hicexplorer.hicPlotMatrix.main(args)
res = compare_images(ROOT + "hicPlotMatrix" + '/small_test_50kb_pearson_pca1_plot_region__colormap_hot_chr2L_15mb-20mb_bw.png', outfile.name, tol=40)
res = compare_images(ROOT + "hicPlotMatrix" + '/small_test_50kb_pearson_pca1_plot_region__colormap_hot_chr2L_15mb-20mb_bw.png', outfile.name, tol=tolerance)
assert res is None, res
if REMOVE_OUTPUT:
os.remove(outfile.name)
2 changes: 1 addition & 1 deletion requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
numpy >= 1.12.1
scipy >= 0.19.0
matplotlib = 2.0.0
matplotlib == 2.1.1
pysam >= 0.11.2
intervaltree >= 2.1.0
biopython >= 1.68
Expand Down
2 changes: 1 addition & 1 deletion setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -95,7 +95,7 @@ def checkProgramIsInstalled(self, program, args, where_to_download,

install_requires_py = ["numpy >= 1.12.1",
"scipy >= 0.19.0",
"matplotlib == 2.0.0",
"matplotlib == 2.1.1",
"pysam >= 0.11.2.2",
"intervaltree >= 2.1.0",
"biopython >= 1.68",
Expand Down

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