Mercurial > repos > mheinzl > fsd_regions

comparison fsd_regions.py @ 1:9ce2b4089c1b draft

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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd_regions commit b9403b3ce2b7a41fa8ee1aa47909152de78cf641
author mheinzl
date Tue, 15 May 2018 13:50:29 -0400
parents b82fdb006304
children 2631864873d7
comparison
equal deleted inserted replaced
0:b82fdb006304 1:9ce2b4089c1b
106 minimumX = numpy.amin(numpy.concatenate(quantAfterRegion)) 106 minimumX = numpy.amin(numpy.concatenate(quantAfterRegion))
107 107
108 ### PLOT ### 108 ### PLOT ###
109 plt.rc('figure', figsize=(11.69, 8.27)) # A4 format 109 plt.rc('figure', figsize=(11.69, 8.27)) # A4 format
110 plt.rcParams['axes.facecolor'] = "E0E0E0" # grey background color 110 plt.rcParams['axes.facecolor'] = "E0E0E0" # grey background color
111 plt.rcParams['xtick.labelsize'] = 12 111 plt.rcParams['xtick.labelsize'] = 14
112 plt.rcParams['ytick.labelsize'] = 12 112 plt.rcParams['ytick.labelsize'] = 14
113 plt.rcParams['patch.edgecolor'] = "black" 113 plt.rcParams['patch.edgecolor'] = "black"
114 fig = plt.figure() 114 fig = plt.figure()
115 plt.subplots_adjust(bottom=0.3) 115 plt.subplots_adjust(bottom=0.3)
116 116
117 colors = ["#6E6E6E", "#0431B4", "#5FB404", "#B40431", "#F4FA58", "#DF7401", "#81DAF5"] 117 colors = ["#6E6E6E", "#0431B4", "#5FB404", "#B40431", "#F4FA58", "#DF7401", "#81DAF5"]
154 for i, s, count in zip(groupUnique, space, quantAfterRegion): 154 for i, s, count in zip(groupUnique, space, quantAfterRegion):
155 plt.text(0.6, 0.05 + s, "{}=\n".format(i), size=11, transform=plt.gcf().transFigure) 155 plt.text(0.6, 0.05 + s, "{}=\n".format(i), size=11, transform=plt.gcf().transFigure)
156 plt.text(0.75, 0.05 + s, "{:,}\n".format(len(count) / 2), size=11, transform=plt.gcf().transFigure) 156 plt.text(0.75, 0.05 + s, "{:,}\n".format(len(count) / 2), size=11, transform=plt.gcf().transFigure)
157 157
158 plt.legend(loc='upper right', fontsize=14, bbox_to_anchor=(0.9, 1), frameon=True) 158 plt.legend(loc='upper right', fontsize=14, bbox_to_anchor=(0.9, 1), frameon=True)
159 plt.title(name1, fontsize=14) 159 #plt.title(name1, fontsize=14)
160 plt.xlabel("No. of Family Members", fontsize=12) 160 plt.xlabel("Family size", fontsize=14)
161 plt.ylabel("Absolute Frequency", fontsize=12) 161 plt.ylabel("Absolute Frequency", fontsize=14)
162 plt.grid(b=True, which="major", color="#424242", linestyle=":") 162 plt.grid(b=True, which="major", color="#424242", linestyle=":")
163 plt.margins(0.01, None) 163 plt.margins(0.01, None)
164 164
165 # plt.savefig("{}_regions.pdf".format(title_file), bbox_inch="tight") 165 # plt.savefig("{}_regions.pdf".format(title_file), bbox_inch="tight")
166 pdf.savefig(fig, bbox_inch="tight") 166 pdf.savefig(fig, bbox_inch="tight")
167 plt.close() 167 plt.close()
168 168
169 output_file.write("Dataset:{}{}\n".format(sep, firstFile)) 169 output_file.write("Dataset:{}{}\n".format(sep, name1))
170 output_file.write("{}AB{}BA\n".format(sep, sep)) 170 output_file.write("{}AB{}BA\n".format(sep, sep))
171 output_file.write("max. family size:{}{}{}{}\n".format(sep, max(map(int, quant_ab)), sep, max(map(int, quant_ba)))) 171 output_file.write("max. family size:{}{}{}{}\n".format(sep, max(map(int, quant_ab)), sep, max(map(int, quant_ba))))
172 output_file.write("absolute frequency:{}{}{}{}\n".format(sep, count[len(count) - 1], sep, count2[len(count2) - 1])) 172 output_file.write("absolute frequency:{}{}{}{}\n".format(sep, count[len(count) - 1], sep, count2[len(count2) - 1]))
173 output_file.write("relative frequency:{}{:.3f}{}{:.3f}\n\n".format(sep, float(count[len(count) - 1]) / sum(count), sep, float(count2[len(count2) - 1]) / sum(count2))) 173 output_file.write("relative frequency:{}{:.3f}{}{:.3f}\n\n".format(sep, float(count[len(count) - 1]) / sum(count), sep, float(count2[len(count2) - 1]) / sum(count2)))
174 output_file.write("total nr. of reads{}{}\n".format(sep, sum(numpy.array(data_array[:, 0]).astype(int)))) 174 output_file.write("total nr. of reads{}{}\n".format(sep, sum(numpy.array(data_array[:, 0]).astype(int))))