Merge branch 'saved-commits'

pyranges · Jun 15, 2024 · 2d52091 · 2d52091
2 parents 7ee6fbd + 84d7359
commit 2d52091
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Showing 12 changed files with 335 additions and 519 deletions.
diff --git a/README.md b/README.md
@@ -358,7 +358,7 @@ prp.print_options()
 |                        |       |         | Provided as a float correspondig to the plot fraction or     |
 |                        |       |         | percentage.                                                  |
 +------------------------+-------+---------+--------------------------------------------------------------+
-|    shrink_threshold    | 0.05  |         | Minimum lenght of an intron in order for it to be shrinked   |
+|    shrink_threshold    | 0.05  |         | Minimum lenght of an intron in order for it to be shrunk   |
 |                        |       |         | while using the shrink feature. When threshold is       |
 |                        |       |         | float, it represents the percentage of the plot space,       |
 |                        |       |         | while an int threshold represents number of positions or     |
@@ -411,7 +411,7 @@ prp.print_options()
 |                        |                    |         | Provided as a float correspondig to the plot fraction or     |
 |                        |                    |         | percentage.                                                  |
 +------------------------+--------------------+---------+--------------------------------------------------------------+
-|    shrink_threshold    |        0.05        |         | Minimum lenght of an intron in order for it to be shrinked   |
+|    shrink_threshold    |        0.05        |         | Minimum lenght of an intron in order for it to be shrunk   |
 |                        |                    |         | while using the shrink feature. When threshold is       |
 |                        |                    |         | float, it represents the percentage of the plot space,       |
 |                        |                    |         | while an int threshold represents number of positions or     |

diff --git a/src/pyranges_plot/core.py b/src/pyranges_plot/core.py
@@ -367,8 +367,8 @@ def format_row(key, value):
                     "title_color",
                     "grid_color",
                     "exon_border",
-                    "shrinked_bkg",
-                    "shrinked_alpha",
+                    "shrunk_bkg",
+                    "x_ticks",
                 ]
             )
         ].copy()
@@ -382,8 +382,7 @@ def format_row(key, value):
                     "arrow_line_width",
                     "arrow_color",
                     "arrow_size",
-                    "arrow_size_min",
-                    "arrow_intron_threshold",
+                    "intron_color",
                 ]
             )
         ].copy()

diff --git a/src/pyranges_plot/introns_off.py b/src/pyranges_plot/introns_off.py
@@ -119,7 +119,7 @@ def introns_resize(df, ts_data, id_col):
     assert to_shrink.sort_values(START_COL).equals(to_shrink), "PyRanges not sorted."
     to_shrink[CUM_DELTA_COL] = to_shrink[DELTA_COL].cumsum()
 
-    # store adjusted coord to plot shrinked intron regions
+    # store adjusted coord to plot shrunk intron regions
     to_shrink[ADJSTART_COL] = to_shrink[
         START_COL
     ] - to_shrink.__cumdelta__.shift().fillna(0)
@@ -145,10 +145,10 @@ def introns_resize(df, ts_data, id_col):
 
 
 def recalc_axis(ts_data, tick_pos_d, ori_tick_pos_d):
-    """Calculate shrinked axis values according to original coordinates."""
+    """Calculate shrunk axis values according to original coordinates."""
 
     for chrom in ts_data.keys():
-        # add to-shrinked reagions limits to axis
+        # add to-shrunk reagions limits to axis
         ori_tick_pos = []
         tick_pos = []
 
@@ -163,7 +163,7 @@ def recalc_axis(ts_data, tick_pos_d, ori_tick_pos_d):
             ]
             cdel = list(ts_data[chrom][CUM_DELTA_COL])
 
-            # update tick positions for shrinked regions and keep original values as names
+            # update tick positions for shrunk regions and keep original values as names
             for i in range(len(pos)):
                 if i == 0:
                     tick_pos.append(pos[i][0])