Merge pull request #223 from deeptools/fix_plotHiC_matrix_on_small_ch…

…romosomes

Improved colorbar scale when log1p options is used.

hicexplorer/HiCMatrix.py

@@ -755,7 +755,7 @@ def convert_to_obs_exp_matrix(self, maxdepth=None, zscore=False, perchr=False):
                 depth = max_depth_in_bins
             else:
                 depth = m_size
-                estimated_size_dense_matrix = m_size**2 * 8
+                estimated_size_dense_matrix = m_size ** 2 * 8
                 if estimated_size_dense_matrix > 100e6:
                     log.info("To compute z-scores a dense matrix is required. This will use \n"
                              "{} Mb of memory.\n To reduce memory use the maxdeph option."

hicexplorer/hicCorrectMatrix.py

@@ -54,8 +54,7 @@ def parse_arguments(args=None):
 """
     )
 
-    parser.add_argument('--version', action='version',
-                        version='%(prog)s {}'.format(__version__))
+    parser.add_argument('--version', action='version', version='%(prog)s {}'.format(__version__))
 
     subparsers = parser.add_subparsers(
         title="Options",
@@ -572,7 +571,7 @@ def main(args=None):
 
     log.info("matrix contains {} data points. Sparsity {:.3f}.".format(
         len(ma.matrix.data),
-        float(len(ma.matrix.data)) / (ma.matrix.shape[0]**2)))
+        float(len(ma.matrix.data)) / (ma.matrix.shape[0] ** 2)))
 
     if args.skipDiagonal:
         ma.diagflat(value=0)

hicexplorer/hicFindTADs.py

@@ -294,7 +294,7 @@ def get_incremental_step_size(min_win_size, max_win_size, start_step_len):
     step = -1
     while 1:
         step += 1
-        inc_step = min_win_size + int(start_step_len * (step**1.5))
+        inc_step = min_win_size + int(start_step_len * (step ** 1.5))
         if step > 1 and inc_step == incremental_step[-1]:
             continue
         if inc_step > max_win_size:

hicexplorer/hicPlotMatrix.py

@@ -14,7 +14,6 @@
 from hicexplorer._version import __version__
 import numpy as np
 import pyBigWig
-from builtins import range
 from past.builtins import zip
 
 import argparse
@@ -138,9 +137,12 @@ def parse_arguments(args=None):
     parserOpt.add_argument('--version', action='version',
                            version='%(prog)s {}'.format(__version__))
 
-    return parser
+    #  Used for automatic testing
+    parserOpt.add_argument('--disable_tight_layout',
+                           help=argparse.SUPPRESS,
+                           action='store_true')
 
-# relabel xticks
+    return parser
 
 
 def relabel_ticks(pXTicks):
@@ -227,16 +229,8 @@ def plotHeatmap(ma, chrBinBoundaries, fig, position, args, cmap, xlabel=None,
         cax = divider.append_axes("right", size="2.5%", pad=0.09)
     else:
         cax = pBigwig['axis_colorbar']
-    if args.log1p:
-        from matplotlib.ticker import LogFormatter
-        formatter = LogFormatter(10, labelOnlyBase=False)
-        # get a useful log scale
-        # that looks like [1, 2, 5, 10, 20, 50, 100, ... etc]
-        aa = np.array([1, 2, 5])
-        tick_values = np.concatenate([aa * 10 ** x for x in range(10)])
-        cbar = fig.colorbar(img3, ticks=tick_values, format=formatter, cax=cax)
-    else:
-        cbar = fig.colorbar(img3, cax=cax)
+
+    cbar = fig.colorbar(img3, cax=cax)
 
     cbar.solids.set_edgecolor("face")  # to avoid white lines in the color bar in pdf plots
     if args.scoreName:
@@ -322,7 +316,7 @@ def plotPerChr(hic_matrix, cmap, args, pBigwig):
         col = idx % chrom_per_row
         if pBigwig:
             inner_grid = gridspec.GridSpecFromSubplotSpec(2, 2, height_ratios=[0.85, 0.15], width_ratios=[0.93, 0.07],
-                                                          subplot_spec=grids[row, col], wspace=0.0, hspace=0.1)
+                                                          subplot_spec=grids[row, col], wspace=0.1, hspace=0.1)
             axis = plt.subplot(inner_grid[0, 0])
             axis_eigenvector = plt.subplot(inner_grid[1, 0])
             axis_scale = plt.subplot(inner_grid[0, 1])
@@ -347,8 +341,6 @@ def plotPerChr(hic_matrix, cmap, args, pBigwig):
                 matrix[mask_nan] = np.nanmin(matrix[mask_nan == False])
                 matrix[mask_inf] = np.nanmin(matrix[mask_inf == False])
 
-                if args.log:
-                    matrix = np.log(matrix)
             except Exception:
                 log.debug("Clearing of matrix failed.")
             log.debug("any nanafter remove of nan: {}".format(np.isnan(matrix).any()))
@@ -357,6 +349,9 @@ def plotPerChr(hic_matrix, cmap, args, pBigwig):
             matrix += 1
             norm = LogNorm()
 
+        elif args.log:
+            norm = LogNorm()
+
         bigwig_info = None
         if pBigwig:
             bigwig_info = {'args': args, 'axis': None, 'axis_colorbar': None, 'nan_bins': hic_matrix.nan_bins}
@@ -560,14 +555,13 @@ def main(args=None):
                 matrix[mask_nan] = np.nanmin(matrix[mask_nan == False])
                 matrix[mask_inf] = np.nanmin(matrix[mask_inf == False])
 
-            if args.log:
-                matrix = np.log(matrix)
-
         log.debug("any nan after remove of nan: {}".format(np.isnan(matrix).any()))
         log.debug("any inf after remove of inf: {}".format(np.isinf(matrix).any()))
         if args.log1p:
             matrix += 1
             norm = LogNorm()
+        elif args.log:
+            norm = LogNorm()
 
         if args.bigwig:
             # increase figure height to accommodate bigwig track
@@ -602,13 +596,14 @@ def main(args=None):
                     args, cmap, xlabel=chrom, ylabel=chrom2,
                     start_pos=start_pos1, start_pos2=start_pos2, pNorm=norm, pAxis=ax1, pBigwig=bigwig_info)
 
-    if args.perChromosome or args.bigwig:
-        try:
-            plt.tight_layout()
-        except UserWarning:
-            log.info("Failed to tight layout. Using regular plot.")
-        except ValueError:
-            log.info("Failed to tight layout. Using regular plot.")
+    if not args.disable_tight_layout:
+        if args.perChromosome or args.bigwig:
+            try:
+                plt.tight_layout()
+            except UserWarning:
+                log.info("Failed to tight layout. Using regular plot.")
+            except ValueError:
+                log.info("Failed to tight layout. Using regular plot.")
 
     plt.savefig(args.outFileName, dpi=args.dpi)
     plt.close(fig)