updating plotting (removed plotly and code clean-up)

pydeeptools/deeptools/plotFingerprint.py

@@ -1,27 +1,18 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import numpy as np
-import argparse
 import sys
-import matplotlib
-matplotlib.use('Agg')
-matplotlib.rcParams['pdf.fonttype'] = 42
-matplotlib.rcParams['svg.fonttype'] = 'none'
-from deeptools import cm  # noqa: F401
+import argparse
+import numpy as np
 import matplotlib.pyplot as plt
 from scipy import interpolate
 from scipy.stats import poisson
 
-import plotly.offline as py
-import plotly.graph_objs as go
-
 import deeptools.countReadsPerBin as countR
 import deeptools.sumCoveragePerBin as sumR
 from deeptools import parserCommon
 from deeptools.utilities import smartLabels
 
-old_settings = np.seterr(all='ignore')
 MAXLEN = 10000000
 
 
@@ -122,8 +113,9 @@ def get_optional_args():
                           'overrides the image format based on the ending '
                           'given via --plotFile '
                           'ending. The available options are: "png", '
-                          '"eps", "pdf", "plotly" and "svg"',
-                          choices=['png', 'pdf', 'svg', 'eps', 'plotly'])
+                          '"eps", "pdf", "jpeg", and "svg"',
+                          choices=['png', 'pdf', 'svg', 'jpeg', 'eps'],
+                          default=None)
 
     optional.add_argument('--plotTitle', '-T',
                           help='Title of the plot, to be printed on top of '
@@ -409,38 +401,18 @@ def main(args=None):
         i = 0
         # matplotlib won't iterate through line styles by itself
         pyplot_line_styles = sum([7 * ["-"], 7 * ["--"], 7 * ["-."], 7 * [":"]], [])
-        plotly_colors = ["#d73027", "#fc8d59", "#f33090", "#e0f3f8", "#91bfdb", "#4575b4"]
-        plotly_line_styles = sum([6 * ["solid"], 6 * ["dot"], 6 * ["dash"], 6 * ["longdash"], 6 * ["dashdot"], 6 * ["longdashdot"]], [])
-        data = []
         for i, reads in enumerate(num_reads_per_bin.T):
             count = np.cumsum(np.sort(reads))
             count = count / count[-1]  # to normalize y from 0 to 1
-            if args.plotFileFormat == 'plotly':
-                trace = go.Scatter(x=x, y=count, mode='lines', name=args.labels[i])
-                trace['line'].update(dash=plotly_line_styles[i % 36], color=plotly_colors[i % 6])
-                data.append(trace)
-            else:
-                j = i % len(pyplot_line_styles)
-                plt.plot(x, count, label=args.labels[i], linestyle=pyplot_line_styles[j])
-                plt.xlabel('rank')
-                plt.ylabel('fraction w.r.t. bin with highest coverage')
-        # set the plotFileFormat explicitly to None to trigger the
-        # format from the file-extension
-        if not args.plotFileFormat:
-            args.plotFileFormat = None
-
-        if args.plotFileFormat == 'plotly':
-            fig = go.Figure()
-            fig.add_traces(data)
-            fig['layout'].update(title=args.plotTitle)
-            fig['layout']['xaxis1'].update(title="rank")
-            fig['layout']['yaxis1'].update(title="fraction w.r.t bin with highest coverage")
-            py.plot(fig, filename=args.plotFile, auto_open=False)
-        else:
-            plt.legend(loc='upper left')
-            plt.suptitle(args.plotTitle)
-            plt.savefig(args.plotFile, bbox_inches=0, format=args.plotFileFormat)
-            plt.close()
+            j = i % len(pyplot_line_styles)
+            plt.plot(x, count, label=args.labels[i], linestyle=pyplot_line_styles[j])
+
+        plt.xlabel('rank')
+        plt.ylabel('fraction w.r.t. bin with highest coverage')
+        plt.legend(loc='upper left')
+        plt.suptitle(args.plotTitle)
+        plt.savefig(args.plotFile, bbox_inches=0, format=args.plotFileFormat)
+        plt.close()
 
     if args.outRawCounts is not None:
         of = open(args.outRawCounts, "w")