Added option to adjust line width using base.cfg #15

schneebergerlab · May 21, 2024 · f6e50b4 · f6e50b4
1 parent 2ac7ba0
commit f6e50b4
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Showing 3 changed files with 26 additions and 8 deletions.
diff --git a/config/base.cfg b/config/base.cfg
@@ -1,17 +1,22 @@
 ## COLOURS and transparency for alignments (syntenic, inverted, translocated, and duplicated)
-syncol:#DEDEDE
+syncol:#CCCCCC
 invcol:#FFA500
 tracol:#9ACD32
 dupcol:#00BBFF
+synlwd:0                ## Line width for syntenic annotations
+invlwd:0.1              ## Line width for inversions
+tralwd:0.1              ## Line width for translocations
+duplwd:0.1              ## Line width for duplications
 alpha:0.8
 
 ## Margins and dimensions:
 chrmar:0.1              ## Adjusts the gap between chromosomes and tracks. Higher values leads to more gap
 exmar:0.1               ## Extra margin at the top and bottom of plot area
+marginchr:0.1         ## Margin between adjacent chromosomes when using --itx
 
 ## LEGEND
-legend:T                    ## To plot legend use T, use F to not plot legend
-genlegcol:-1                ## Number of columns for genome legend, set -1 for automatic setup
-bbox:0,1.01,0.5,0.3         ## [Left edge, bottom edge, width, height]
-## bbox:[0, 1.1, 0.5, 0.3]  ## For vertical chromosomes (using -v option)
-bboxmar:0.5                 ## Margin between genome and annotation legends
+legend:T                ## To plot legend use T, use F to not plot legend
+genlegcol:-1            ## Number of columns for genome legend, set -1 for automatic setup
+bbox:0,1.01,0.5,0.3		## [Left edge, bottom edge, width, height]
+bbox_v:0,1.1,0.5,0.3	## For vertical chromosomes (using -v option)
+bboxmar:0.5             ## Margin between genome and annotation legends
diff --git a/example/base.cfg b/example/base.cfg
@@ -3,11 +3,16 @@ syncol:#CCCCCC
 invcol:#FFA500
 tracol:#9ACD32
 dupcol:#00BBFF
+synlwd:0                ## Line width for syntenic annotations
+invlwd:0.1              ## Line width for inversions
+tralwd:0.1              ## Line width for translocations
+duplwd:0.1              ## Line width for duplications
 alpha:0.8
 
 ## Margins and dimensions:
 chrmar:0.1              ## Adjusts the gap between chromosomes and tracks. Higher values leads to more gap
 exmar:0.1               ## Extra margin at the top and bottom of plot area
+marginchr:0.1         ## Margin between adjacent chromosomes when using --itx
 
 ## LEGEND
 legend:T                ## To plot legend use T, use F to not plot legend

diff --git a/plotsr/scripts/func.py b/plotsr/scripts/func.py
@@ -194,6 +194,10 @@ def readbasecfg(f, v):
     cfg['invcol'] = '#FFA500'
     cfg['tracol'] = '#9ACD32'
     cfg['dupcol'] = '#00BBFF'
+    cfg['synlwd'] = 0
+    cfg['invlwd'] = 0.1
+    cfg['tralwd'] = 0.1
+    cfg['duplwd'] = 0.1
     cfg['alpha'] = 0.8
     # Set chromosome margins
     cfg['chrmar'] = 0.1
@@ -230,7 +234,7 @@ def readbasecfg(f, v):
                     logger.error("Error in using colour: {} for {}. Use correct hexadecimal colours or named colours defined in matplotlib (https://matplotlib.org/stable/gallery/color/named_colors.html). Using default value.".format(line[1], line[0]))
                     continue
                 cfg[line[0]] = line[1]
-            elif line[0] in ['alpha', 'chrmar', 'exmar', 'bboxmar', 'genlegcol', 'marginchr']:
+            elif line[0] in ['synlwd', 'invlwd', 'tralwd', 'duplwd', 'alpha', 'chrmar', 'exmar', 'bboxmar', 'genlegcol', 'marginchr']:
                 try:
                     float(line[1])
                 except ValueError:
@@ -1572,6 +1576,10 @@ def annotodict(anno):
                    'INV': cfg['invcol'],
                    'TRANS': cfg['tracol'],
                    'DUP': cfg['dupcol']}
+        lwddict = {'SYN': cfg['synlwd'],
+                   'INV': cfg['invlwd'],
+                   'TRANS': cfg['tralwd'],
+                   'DUP': cfg['duplwd']}
         # df['col'] = [coldict[c] for c in df['type']]
         labdict = {'SYN': 'Syntenic', 'INV': 'Inversion', 'TRANS': 'Translocation', 'DUP': 'Duplication'}
         df['lab'] = [labdict[c] for c in df['type']]
@@ -1586,7 +1594,7 @@ def annotodict(anno):
         for row in df.itertuples():
             if row.anno == '-':
                 newcol.append(coldict[row.type])
-                newlw.append(0 if row.type == 'SYN' else 0.1)
+                newlw.append(lwddict[row.type])
                 newz.append(0 if row.type == 'SYN' else 1)
             else:
                 anno = annotodict(row.anno)