def plot_coords_quads(self): print ("plots dir is: " + self.plots_dir) if not os.path.exists(self.plots_dir): os.mkdir(self.plots_dir) # os.chdir(self.treehome) self.setTopNum() print "TopNum is: " + str(self.topNum) for i in range(1, self.topNum + 1): os.chdir(self.plots_dir) logplot = make_rplotscript( self.coords_dir, self.coords_filepref + str(i) + ".txt", self.tree_name + " Topology " + str(i) + " Logmap", aspect_ratio=1, outdir=self.plots_dir, mean=False, majority=False, ) logplot.rplot() # logplot.setNormFile(self.coords_prefix + str(i) + "_norms.txt") # logplot.rplotnorm() command = self.Rpath + " " + self.coords_dir + "/" + self.coords_filepref + str(i) + ".r" # command = 'C:\\Rstuff\\R-3.2.0\\bin\\Rscript.exe ' + self.coords_dir + "/" + self.coords_filepref + str(i) + '.r' subprocess.call(command.split()) # normcommand = 'C:\\Rstuff\\R-3.2.0\\bin\\Rscript.exe ' + self.coords_dir +"/" + self.coords_filepref + str(i) + "_norm3D.r" # subprocess.call(normcommand.split()) else: print "Quadrants already plotted - skipping quadrant creation"
def plot_coords_all(self): os.chdir(self.treehome) if not os.path.exists(self.plots_all): allplot = make_rplotscript( self.treehome, self.all_topos_coords_centre, self.tree_name + " All Topologies Relative to Centre 1 Logmap", aspect_ratio=1, outdir=self.treehome, mean=False, majority=False, ) allplot.rplot() # allplot.setNormFile(self.treehome + self.tree_name + "_" + self.model + "_norms.txt") # allplot.rplotnorm() # command = 'C:\\Rstuff\\R-3.2.0\\bin\\Rscript.exe ' + self.treehome + self.all_topos_coords_centre[0:-4] + self.ordered + '.r' command = self.Rpath + " " + self.treehome + "/" + self.all_topos_coords_centre[0:-4] + self.ordered + ".r" print ("command is: " + command) subprocess.call(command.split()) # normcommand = 'C:\\Rstuff\\R-3.2.0\\bin\\Rscript.exe ' + self.treehome + self.all_topos_coords_centre[0:-4] + self.ordered + '_norm3D.r' # subprocess.call(normcommand.split()) else: print "All topologies already plotted - skipping plot creation"
''' # Make the tree file including the mean and majority tree: if not os.path.exists(tree_file_mn_1st): infile1 = open(tree_file_mn_1st, 'r') #infile2 = open(majority_tree_file, 'r') infile3 = open(tree_file,'r') outfile = open(tree_file_mn_1st, 'w') outfile.write(infile1.readline() + "\n") infile1.close() #outfile.write(infile2.readline() + "\n") #infile2.close() for line in infile3: outfile.write(line) infile3.close() outfile.close() # Find the coordinates for mean, majority, and all trees: if not os.path.exists(all_coords_mn): command = 'java -jar ' + analysis_version + ' -u -a log_map -o ' + all_coords_mn + ' -f ' + center_tree_file + " " + tree_file_mn_1st subprocess.call(command.split()) # Generate the R script for the trees: # This version gets all three: #newbase_r = make_rplotscript(all_coords_mn_maj,"Trees with Base, Mean & Majority","log",1,True,True) newbase_r = make_rplotscript(all_coords_mn,"Trees with Base & Mean","log",1,True,False) newbase_r.set_base(1,10) newbase_r.rplot(True)