def plotMDS(tree, treehome, model, mn=False, maj=False):
os.chdir(treehome)
model_label = "_" + model + "_"
titlest = "All trees with base "
titleend = "under MDS"
if (mn == True and maj == True):
suffix = "_mn_maj_"
titlest = titlest + " mean and majority trees "
elif (mn == True):
suffix = "_mn_"
titlest = titlest + " and mean tree "
else:
suffix = "_"
if not os.path.exists(tree + suffix + "2D.r"):
temp = make_rMDSscript(tree, tree + model_label + "dist_matrix", titlest + titleend, 1, mn, maj)
temp.plot_MDS(2)
command = "rscript " + tree + "_2D.r"
call(command.split())
else:
print ("MDS plots already exist for 2D trees - skipping")
call(command.split())
else:
print ("Distance file already exists for base mean maj - skipping running GTP")
if not os.path.exists(trees_mn_maj_dist_matrix):
get_diss_matrix(trees_mn_maj_distances,trees_mn_maj_dist_matrix,"symmetric")
else:
print ("Distance matrix already exists for base mean maj- skipping")
# Create R script for MDS
# Part one: geodesic
# 2D:
if not os.path.exists(tree + "_2D.r"):
all_trees = make_rMDSscript(tree, tree_dist_matrix, "All trees and base tree under MDS", 1)
all_trees.plot_MDS(2)
command = "rscript " + tree + "_2D.r"
call(command.split())
else:
print ("MDS plots already exist for 2D trees - skipping")
# Second, all trees with the mean:
if not os.path.exists(tree + "_mean" + "_2D.r"):
all_trees_and_mean = make_rMDSscript(tree, trees_mn_dist_matrix, "All trees, base tree, and mean tree under MDS",1,mean=True)
all_trees_and_mean.plot_MDS(2)
command = "rscript " + tree + "_mean" + "_2D.r"
call(command.split())
# Third, all trees with mean and majority:
if not os.path.exists(tree + "_mean_maj" + "_2D.r"):
