Editable text in pdf format outputs and customizing colors

plot_cladogram.py

@@ -6,6 +6,8 @@
 from pylab import *
 from lefse import *
 import numpy as np
+# support outputting editable texts in pdf
+matplotlib.rcParams['pdf.fonttype'] = 42
 
 colors = ['r','g','b','m','c',[1.0,0.5,0.0],[0.0,1.0,0.0],[0.33,0.125,0.0],[0.75,0.75,0.75],'k']
 dark_colors = [[0.4,0.0,0.0],[0.0,0.2,0.0],[0.0,0.0,0.4],'m','c',[1.0,0.5,0.0],[0.0,1.0,0.0],[0.33,0.125,0.0],[0.75,0.75,0.75],'k']
@@ -43,6 +45,7 @@ def read_params(args):
     parser.add_argument('input_file', metavar='INPUT_FILE', type=str, help="tab delimited input file")
     parser.add_argument('output_file', metavar='OUTPUT_FILE', type=str, help="the file for the output image")
     parser.add_argument('--clade_sep',dest="clade_sep", type=float, default=1.5)
+    parser.add_argument('--customized_colors',dest="customized_colors", help="Accept a list of colors in format like <red,blue,yellow>", type=str, default="")
     parser.add_argument('--max_lev',dest="max_lev", type=int, default=-1)
     parser.add_argument('--max_point_size',dest="max_point_size", type=float, default=6.0)
     parser.add_argument('--min_point_size',dest="min_point_size", type=float, default=1)
@@ -334,13 +337,15 @@ def get_col_attr(x):
         if l2 != None:
             for o in l2.findobj(get_col_attr):
                     o.set_color(params['fore_color'])
-    # add bbox to deal with legnd overflow
+    # add bbox_inches to deal with legnd overflow
     plt.savefig(out_file,format=params['format'],facecolor=params['back_color'],edgecolor=params['fore_color'],dpi=params['dpi'], bbox_inches='tight')
     plt.close()    
 
 if __name__ == '__main__':
     params = read_params(sys.argv)
     params['fore_color'] = 'w' if params['back_color'] == 'k' else 'k'
+    if params['customized_colors']:
+        colors = [i.strip() for i in params['customized_colors'].split(',')]
     clad_tree = read_data(params['input_file'],params)    
     draw_tree(params['output_file'],clad_tree,params)
 

plot_features.py

@@ -6,6 +6,8 @@
 from lefse import *
 import random as rand
 
+matplotlib.rcParams['pdf.fonttype'] = 42 
+
 colors = ['r','g','b','m','c']
 
 def read_params(args):
@@ -23,6 +25,7 @@ def read_params(args):
 	parser.add_argument('--subcl_mean',dest="subcl_mean", type=str, choices=["y","n"], default="y")
 	parser.add_argument('--subcl_median',dest="subcl_median", type=str, choices=["y","n"], default="y")
 	parser.add_argument('--font_size',dest="font_size", type=str, default="10")
+	parser.add_argument('--customized_colors',dest="customized_colors", type=str, default="",help="Accept a list of colors in format like <red,blue,yellow>")
 	parser.add_argument('-n',dest="unused", metavar="flt", type=float, default=-1.0,help="unused")
 	parser.add_argument('--format', dest="format", default="png", choices=["png","pdf","svg"], type=str, help="the format for the output file")
 	parser.add_argument('-f', dest="f", default="diff", choices=["all","diff","one"], type=str, help="wheter to plot all features (all), only those differentially abundant according to LEfSe or only one (the one given with --feature_name) ")
@@ -91,6 +94,7 @@ def plot(name,k_n,feat,params):
 			pos = arange(fr,to)
 			max_x = to
 			col = colors[j%len(colors)]
+			#print(col)
 			vv = [v1/norm for v1 in val]
 			median = numpy.median(vv)
 			mean = numpy.mean(vv)
@@ -142,6 +146,7 @@ def get_edgecol_attr(x):
 	params['fore_color'] = 'w' if params['back_color'] == 'k' else 'k'
 	features = read_data(params['input_file_1'],params['input_file_2'],params)
 	if params['archive'] == "zip": file = zipfile.ZipFile(params['output_file'], "w")
+	if params['customized_colors']: colors = [i.strip() for i in params['customized_colors'].split(',')] 
 	for k,f in features.items():
 		print("Exporting ", k)
 		if params['archive'] == "zip":

plot_res.py

@@ -6,6 +6,8 @@
 from pylab import *
 from collections import defaultdict
 
+matplotlib.rcParams['pdf.fonttype'] = 42 
+
 from lefse import *
 import argparse
 
@@ -17,6 +19,7 @@ def read_params(args):
     parser.add_argument('output_file', metavar='OUTPUT_FILE', type=str, help="the file for the output image")
     parser.add_argument('--feature_font_size', dest="feature_font_size", type=int, default=7, help="the file for the output image")
     parser.add_argument('--format', dest="format", choices=["png","svg","pdf"], default='png', type=str, help="the format for the output file")
+    parser.add_argument('--customized_colors',dest="customized_colors", help="Accept a list of colors in format like <red,blue,yellow>", type=str, default="")
     parser.add_argument('--dpi',dest="dpi", type=int, default=72)
     parser.add_argument('--title',dest="title", type=str, default="")
     parser.add_argument('--title_font_size',dest="title_font_size", type=str, default="12")
@@ -172,6 +175,9 @@ def plot_histo_ver(path,params,data,report_features):
 if __name__ == '__main__':
     params = read_params(sys.argv)
     params['fore_color'] = 'w' if params['back_color'] == 'k' else 'k'
+    # support customized_colors
+    if params['customized_colors']:
+        colors = [i.strip() for i in params['customized_colors'].split(',')]
     data = read_data(params['input_file'],params['output_file'],params['otu_only'])
     if params['orientation'] == 'v': plot_histo_ver(params['output_file'],params,data,params['report_features'])
     else: plot_histo_hor(params['output_file'],params,data,len(data['cls']) == 2,params['report_features'])