Fixing the docs

deeptools · Jul 27, 2021 · ed804ad · ed804ad
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diff --git a/docs/conf.py b/docs/conf.py
@@ -28,9 +28,12 @@
                 'matplotlib', 'matplotlib.pyplot', 'matplotlib.gridspec', 'matplotlib.ticker',
                 'matplotlib.textpath', 'matplotlib.patches', 'matplotlib.colors', 'matplotlib.cm',
                 'mpl_toolkits', 'mpl_toolkits.axisartist', 'mpl_toolkits.mplot3d', 'mpl_toolkits.axes_grid1',
-                'Bio', 'Bio.Seq', 'pyBigWig', 'tables', 'pytables', 'future', 'past', 'past.builtins',
+                'Bio.Seq', 'pyBigWig', 'tables', 'pytables', 'future', 'past', 'past.builtins',
                 'future.utils', 'cooler', 'logging', 'unidecode', 'hic2cool', 'hicmatrix', 'hicmatrix.HiCMatrix',
-                'hicmatrix.lib', 'krbalancing', 'fit_nbinom', 'pybedtools', 'graphviz', 'hyperopt', 'sklearn', 'sklearn.cluster']
+                'hicmatrix.lib', 'krbalancing', 'fit_nbinom', 'pybedtools', 'graphviz', 'hyperopt', 'sklearn', 'sklearn.cluster',
+                'h5py', 'numpy.random', 'sklearn', 'sklearn.model_selection', 'matplotlib.backends', 'sklearn.preprocessing',
+                'matplotlib.backends.backend_agg', 'cleanlab.classification', 'imblearn.under_sampling', 'sklearn.ensemble',
+                'sklearn.metrics', 'sklearn.impute', 'tarfile']
 
 for mod_name in MOCK_MODULES:
     sys.modules[mod_name] = Mock()

diff --git a/docs/content/News.rst b/docs/content/News.rst
@@ -148,7 +148,7 @@ Release 3.4.2
 
 Preprint
 --------
-**6 March 2020*
+**6 March 2020**
 
 The preprint of the loop detection algorithm is online via biorXiv: `<https://www.biorxiv.org/content/10.1101/2020.03.05.979096v1>`_
 

diff --git a/docs/content/list-of-tools.rst b/docs/content/list-of-tools.rst
@@ -51,6 +51,8 @@ Tools for TADs processing
     tools/hicDifferentialTAD
     tools/hicMergeTADbins
     tools/hicInterIntraTAD
+    tools/hicTrainTADClassifier
+    tools/hicTADClassifier
 
 
 Tools for Hi-C and TADs visualization
@@ -115,7 +117,11 @@ For single-cell Hi-C data analysis please use `scHiCExplorer <https://schicexplo
 |:ref:`hicDifferentialTAD`             | analysis         | two Hi-C matrices                 | two diff_tad files: accepted H0 and         | Identifies differential Topologically Associating Domains (TADs) between          |
 |                                      |                  | one TAD domain file               | rejected H0. Similar to BED6                | two Hi-C matrices                                                                 |
 +--------------------------------------+------------------+-----------------------------------+---------------------------------------------+-----------------------------------------------------------------------------------+
-|:ref:`hicInterIntraTAD`             | analysis         | Hi-C matrix, TAD boundaries       | data file and a plot                        | Computes and extracts TAD data. Creates a plot for the inter/intra contact ratio. |
+|:ref:`hicInterIntraTAD`               | analysis         | Hi-C matrix, TAD boundaries       | data file and a plot                        | Computes and extracts TAD data. Creates a plot for the inter/intra contact ratio. |
++--------------------------------------+------------------+-----------------------------------+---------------------------------------------+-----------------------------------------------------------------------------------+
+|:ref:`hicTrainTADClassifier`          | analysis         | Hi-C matrix, TAD boundaries       | ML model for hicTADClassifier               | Computes a ML model for hicTADClassifier.                                         |
++--------------------------------------+------------------+-----------------------------------+---------------------------------------------+-----------------------------------------------------------------------------------+
+|:ref:`hicTADClassifier`               | analysis         | Hi-C matrix, (ML model)           | predicted TAD boundaries                    | Computes TAD boundaries based on a ML model from hicTrainTADClassifier            |
 +--------------------------------------+------------------+-----------------------------------+---------------------------------------------+-----------------------------------------------------------------------------------+
 |:ref:`hicPlotMatrix`                  | visualization    | hicMatrix object                  | a heatmap of Hi-C contacts                  | Plots a Hi-C matrix as a heatmap                                                  |
 +--------------------------------------+------------------+-----------------------------------+---------------------------------------------+-----------------------------------------------------------------------------------+

diff --git a/docs/content/tools/hicPlotSVL.rst b/docs/content/tools/hicPlotSVL.rst
@@ -8,6 +8,9 @@ hicPlotSVL
 
 Description
 ^^^^^^^^^^^
+.. argparse::
+    :ref: hicexplorer.hicPlotSVL.parse_arguments
+    :prog: hicPlotSVL
 
 hicPlotSVL computes the ratio between short range and long range contacts per chromosome independently. Per sample one box plot is created and, if more than one sample is given,
 the computed ratios are assumed to be one distribution and a Wilcoxon rank-sum test under H0 'distributions are equal' is computed. All used data is written to a third raw data file.

diff --git a/docs/content/tools/hicTrainTADClassifier.rst b/docs/content/tools/hicTrainTADClassifier.rst
@@ -1,7 +1,7 @@
 .. _hicTrainTADClassifier:
 
 hicTrainTADClassifier
-==================
+=====================
 
 .. contents:: 
     :local:

diff --git a/docs/index.rst b/docs/index.rst
@@ -67,7 +67,8 @@ tool                                 description
 :ref:`hicHyperoptDetectLoops`        Search for optimal hicDectectLoops parameters
 :ref:`hicHyperoptDetectLoopsHiCCUPS` Search for optimal Juicer HiCCUPS parameters
 :ref:`hicInterIntraTAD`              Extras and computes inter and intra TAD data
-
+:ref:`hicTrainTADClassifier`         Train a classifier to predict TADs with hicTADClassifier
+:ref:`hicTADClassifier`              Predict TAD boundaries with hicTADClassifier
 ==================================== ==========================================================================================================================================================
 
 Getting Help

diff --git a/hicexplorer/chicPlotViewpoint.py b/hicexplorer/chicPlotViewpoint.py
@@ -17,7 +17,6 @@
 import matplotlib.gridspec as gridspec
 from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
 import matplotlib as mpl
-mpl.rcParams['pdf.fonttype'] = 42
 import hicmatrix.HiCMatrix as hm
 from hicexplorer import utilities
 from hicexplorer._version import __version__
@@ -298,6 +297,8 @@ def plot_images(pInteractionFileList, pHighlightDifferentialRegionsFileList, pBa
 
 def main(args=None):
     args = parse_arguments().parse_args(args)
+    mpl.rcParams['pdf.fonttype'] = 42
+
     viewpointObj = Viewpoint()
     background_data = None
 

diff --git a/hicexplorer/chicQualityControl.py b/hicexplorer/chicQualityControl.py
@@ -11,8 +11,7 @@
 import matplotlib
 matplotlib.use('Agg')
 import matplotlib.pyplot as plt
-import matplotlib as mpl
-mpl.rcParams['pdf.fonttype'] = 42
+
 from hicmatrix import HiCMatrix as hm
 from hicexplorer._version import __version__
 from .lib import Viewpoint
@@ -126,7 +125,7 @@ def compute_sparsity(pReferencePoints, pViewpointObj, pArgs, pQueue):
 
 def main(args=None):
     args = parse_arguments().parse_args(args)
-
+    matplotlib.rcParams['pdf.fonttype'] = 42
     viewpointObj = Viewpoint()
     referencePoints, _ = viewpointObj.readReferencePointFile(
         args.referencePoints)

diff --git a/hicexplorer/hicAggregateContacts.py b/hicexplorer/hicAggregateContacts.py
@@ -10,8 +10,7 @@
 import matplotlib.gridspec as gridspec
 import matplotlib.cm as cm
 from mpl_toolkits.mplot3d import Axes3D
-import matplotlib as mpl
-mpl.rcParams['pdf.fonttype'] = 42
+
 # from scipy.cluster.vq import vq, kmeans
 # from scipy.cluster.hierarchy import fcluster, linkage
 import sklearn.cluster as skclust
@@ -859,6 +858,8 @@ def plot_diagnostic_heatmaps(clustered_info, M_half, args):
 
 def main(args=None):
     args = parse_arguments().parse_args(args)
+    matplotlib.rcParams['pdf.fonttype'] = 42
+
     ma = hm.hiCMatrix(args.matrix)
     ma.maskBins(ma.nan_bins)
     ma.matrix.data[np.isnan(ma.matrix.data)] = 0

diff --git a/hicexplorer/hicCompartmentalization.py b/hicexplorer/hicCompartmentalization.py
@@ -3,8 +3,7 @@
 import pandas as pd
 import matplotlib
 import matplotlib.pyplot as plt
-import matplotlib as mpl
-mpl.rcParams['pdf.fonttype'] = 42
+
 import logging
 from hicmatrix import HiCMatrix as hm
 from hicexplorer._version import __version__
@@ -177,6 +176,7 @@ def main(args=None):
     Main function to generate the polarization plot.
     """
     args = parse_arguments().parse_args(args)
+    matplotlib.rcParams['pdf.fonttype'] = 42
 
     pc1 = pd.read_table(args.pca, header=None, sep="\t",
                         dtype={0: "object", 1: "Int64", 2: "Int64", 3: "float32"})

diff --git a/hicexplorer/hicCorrectMatrix.py b/hicexplorer/hicCorrectMatrix.py
@@ -21,8 +21,7 @@
 import matplotlib.pyplot as plt
 import matplotlib.gridspec as gridspec
 from matplotlib.ticker import MultipleLocator, FormatStrFormatter
-import matplotlib as mpl
-mpl.rcParams['pdf.fonttype'] = 42
+import matplotlib
 import numpy as np
 debug = 0
 
@@ -591,6 +590,8 @@ def filter_by_zscore(hic_ma, lower_threshold, upper_threshold, perchr=False):
 
 def main(args=None):
     args = parse_arguments().parse_args(args)
+    matplotlib.rcParams['pdf.fonttype'] = 42
+
     if args.verbose:
         log.setLevel(logging.INFO)
 

diff --git a/hicexplorer/hicCorrelate.py b/hicexplorer/hicCorrelate.py
@@ -16,7 +16,7 @@
 # for plotting
 from matplotlib import use as mplt_use
 import matplotlib as mpl
-mpl.rcParams['pdf.fonttype'] = 42
+
 mplt_use('Agg')
 
 import matplotlib.pyplot as plt
@@ -247,7 +247,7 @@ def get_vectors(mat1, mat2):
 def main(args=None):
 
     args = parse_arguments().parse_args(args)
-
+    mpl.rcParams['pdf.fonttype'] = 42
     if args.labels and len(args.matrices) != len(args.labels):
         log.error("The number of labels does not match the number of matrices.")
         exit(0)

diff --git a/hicexplorer/hicInterIntraTAD.py b/hicexplorer/hicInterIntraTAD.py
@@ -6,7 +6,6 @@
 from copy import deepcopy
 import matplotlib.pyplot as plt
 import matplotlib as mpl
-mpl.rcParams['pdf.fonttype'] = 42
 import logging
 log = logging.getLogger(__name__)
 from hicmatrix import HiCMatrix as hm
@@ -271,6 +270,7 @@ def computeInterIntraTADs(pMatrix, pDomainList, pCoolOrH5, pThreadId, pQueue):
 
 def main(args=None):
     args = parse_arguments().parse_args(args)
+    mpl.rcParams['pdf.fonttype'] = 42
 
     # read domains file
     domains_df = readDomainBoundaries(args.tadDomains)

diff --git a/hicexplorer/hicPlotAverageRegions.py b/hicexplorer/hicPlotAverageRegions.py
@@ -9,7 +9,6 @@
 import matplotlib
 matplotlib.use('Agg')
 import matplotlib as mpl
-mpl.rcParams['pdf.fonttype'] = 42
 from matplotlib.colors import LogNorm
 import matplotlib.pyplot as plt
 import numpy as np
@@ -76,6 +75,7 @@ def parse_arguments(args=None):
 def main(args=None):
 
     args = parse_arguments().parse_args(args)
+    mpl.rcParams['pdf.fonttype'] = 42
 
     matrix = load_npz(args.matrix)
 

diff --git a/hicexplorer/hicPlotDistVsCounts.py b/hicexplorer/hicPlotDistVsCounts.py
@@ -13,7 +13,6 @@
 matplotlib.use('Agg')
 import matplotlib.pyplot as plt
 import matplotlib as mpl
-mpl.rcParams['pdf.fonttype'] = 42
 
 from collections import OrderedDict
 from past.builtins import zip
@@ -406,6 +405,8 @@ def main(args=None):
     """
 
     args = parse_arguments().parse_args(args)
+    mpl.rcParams['pdf.fonttype'] = 42
+
     mean_dict = OrderedDict()
     matrix_sum = {}
     if args.labels is None:

diff --git a/hicexplorer/hicPlotMatrix.py b/hicexplorer/hicPlotMatrix.py
@@ -7,7 +7,6 @@
 from matplotlib.colors import LogNorm
 import matplotlib
 import matplotlib as mpl
-mpl.rcParams['pdf.fonttype'] = 42
 import argparse
 from past.builtins import zip
 import pyBigWig
@@ -637,6 +636,8 @@ def bigwig_axes_config(pArgs, pBigWigInfo):
 
 def main(args=None):
     args = parse_arguments().parse_args(args)
+    mpl.rcParams['pdf.fonttype'] = 42
+
     if args.title:
         args.title = remove_non_ascii(args.title)
 

diff --git a/hicexplorer/hicPlotSVL.py b/hicexplorer/hicPlotSVL.py
@@ -12,7 +12,6 @@
 import matplotlib.pyplot as plt
 import matplotlib.patches as mpatches
 import matplotlib as mpl
-mpl.rcParams['pdf.fonttype'] = 42
 from scipy.stats import ranksums
 
 from hicmatrix import HiCMatrix as hm
@@ -132,6 +131,8 @@ def compute_relation_short_long_range(pHiCMatrix, pChromosomes, pDistance, pIsCo
 def main(args=None):
 
     args = parse_arguments().parse_args(args)
+    mpl.rcParams['pdf.fonttype'] = 42
+
     short_v_long_range = []
     sum_smaller = []
     sum_greater = []

diff --git a/hicexplorer/hicPlotViewpoint.py b/hicexplorer/hicPlotViewpoint.py
@@ -10,7 +10,6 @@
 matplotlib.use('Agg')
 import matplotlib.pyplot as plt
 import matplotlib as mpl
-mpl.rcParams['pdf.fonttype'] = 42
 import os
 from hicexplorer._version import __version__
 
@@ -106,6 +105,8 @@ def getViewpointValues(pMatrix, pReferencePoint, pChromViewpoint, pRegion_start,
 
 def main(args=None):
     args = parse_arguments().parse_args(args)
+    mpl.rcParams['pdf.fonttype'] = 42
+
     log.warning('This tool is deprecated. Please use chicViewpoint, chicViewpointBackgroundModel and chicPlotViewpoint.')
     if args.region:
 

diff --git a/hicexplorer/hicPrepareQCreport.py b/hicexplorer/hicPrepareQCreport.py
@@ -10,7 +10,6 @@
 matplotlib.use('Agg')
 import matplotlib.pyplot as plt
 import matplotlib as mpl
-mpl.rcParams['pdf.fonttype'] = 42
 from hicexplorer._version import __version__
 
 import logging
@@ -261,6 +260,8 @@ def main(args=None):
     """
 
     args = parse_arguments().parse_args(args)
+    mpl.rcParams['pdf.fonttype'] = 42
+
     params = dict()
     make_sure_path_exists(args.outputFolder)
     for fh in args.logfiles: