Added a new base.cfg option maxl for manual adjustment of the maxim…

…um x coordinate on the plot (#69)

config/base.cfg

@@ -14,13 +14,15 @@ chrmar:0.1              ## Adjusts the gap between chromosomes and tracks. Highe
 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
 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
 
+## Tracks
+norm:T                  ## For each chromosome, independently normalise the y-axis of tracks. Use T for normalising independently, and F to normalise based on max value across all chromosomes
 
-## Tracks:
-norm:T                 ## For each chromosome, independently normalise the y-axis of tracks. Use T for normalising independently, and F to normalise based on max value across all chromosomes
+## Axis
+maxl:-1                 ## Manually set maximum chromosome position. Use `-1` for automatic selection. Does not work with --itx

example/base.cfg

@@ -14,13 +14,15 @@ chrmar:0.1              ## Adjusts the gap between chromosomes and tracks. Highe
 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
 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
 
+## Tracks
+norm:T                  ## For each chromosome, independently normalise the y-axis of tracks. Use T for normalising independently, and F to normalise based on max value across all chromosomes
 
-## Tracks:
-norm:T                 ## For each chromosome, independently normalise the y-axis of tracks. Use T for normalising independently, and F to normalise based on max value across all chromosomes
+## Axis
+maxl:-1                 ## Manually set maximum chromosome position. Use `-1` for automatic selection. Does not work with --itx

plotsr/scripts/func.py

@@ -215,6 +215,9 @@ def readbasecfg(f, v):
     # track properties
     cfg['norm'] = 'T'
 
+    # axis properties
+    cfg['maxl'] = -1
+
 
     if f == '':
         return cfg
@@ -238,7 +241,7 @@ 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 ['synlwd', 'invlwd', 'tralwd', 'duplwd', 'alpha', 'chrmar', 'exmar', 'bboxmar', 'genlegcol', 'marginchr']:
+            elif line[0] in ['synlwd', 'invlwd', 'tralwd', 'duplwd', 'alpha', 'chrmar', 'exmar', 'bboxmar', 'genlegcol', 'marginchr', 'maxl']:
                 try:
                     float(line[1])
                 except ValueError:

plotsr/scripts/plotsr.py

@@ -226,6 +226,8 @@ def plotsr(args):
         MCHR = 0.01     # TODO : read spacing between neighbouring chromosome from config file
         maxchr = max([sum(chrlengths[i][1].values()) for i in range(len(chrlengths))])
         maxl = int(maxchr/(MCHR + 1 - (MCHR*len(chrgrps))))
+    elif cfg['maxl'] != -1:
+        minl, maxl = 0, cfg['maxl']
     elif REG is None:
         minl, maxl = 0, -1
     else: