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#python create_heatmaps.py matrixFolder simkaRscriptFolder
import os
from os import listdir
from os.path import isfile, join, splitext
import sys, argparse
parser = argparse.ArgumentParser()
parserFile = parser.add_argument_group("in/out options")
parserMetadata = parser.add_argument_group("metadata options")
parserVisualization = parser.add_argument_group("visualization options")
parserFile.add_argument('-in', action="store", dest="input_dir", help="simka result directory containing distance matrices", required=True)
parserFile.add_argument('-out', action="store", dest="output_dir", help="output directory for figures", required=True)
parserFile.add_argument('-width', action="store", dest="width", help="width of figures in inches", default="7")
parserFile.add_argument('-height', action="store", dest="height", help="height of figures in inches", default="7")
parserFile.add_argument('-format', action="store", dest="format", help="output format (pdf or png)", default="png")
parserMetadata.add_argument('-metadata-in', action="store", dest="metadata_filename", help="filename containing metadata of datasets in csv format (separator=;)")
parserMetadata.add_argument('-metadata-variable', action="store", dest="metadata_variable", help="the name of the variable you want to use in metadata table (column name)")
parserVisualization.add_argument('-heatmap', action="store_true", dest="want_heatmap", help="compute and output heatmap")
parserVisualization.add_argument('-tree', action="store_true", dest="want_tree", help="compute and output hierachical clustering as a dendrogram")
parserVisualization.add_argument('-pca', action="store_true", dest="want_pca", help="compute and output pca (more precisely mds/PCoA)")
parserVisualization.add_argument('-pca-axis-1', action="store", dest="pca_axis_1", help="the number of the first axis of the PCA (only used if -pca)", default="1")
parserVisualization.add_argument('-pca-axis-2', action="store", dest="pca_axis_2", help="the number of the second axis of the PCA (only used if -pca)", default="2")
args = parser.parse_args()
matrix = {}
#matrix = {
#"presenceAbsence_sorensen": [],
#"presenceAbsence_jaccard": [],
#"abundance_jaccard": [],
#"abundance_brayCurtis": [],
#}
def add_metadata_args(command):
command += " " + args.width
command += " " + args.height
command += " " + args.format
if args.metadata_filename != None:
if args.metadata_variable == None:
print("Please specify wanted variable name (column name) in metadata table with option -metadata-variable")
exit(1)
command += " " + args.metadata_filename + " " + args.metadata_variable
return command
def outputHeatmap(outputFilename, matrixAsymFilename, matrixSymFilename):
if not args.want_heatmap: return
#asymFilename = matrixAsymFilename + _outputFilenameSuffix + ".csv";
# normFilename = matrixNormFilename + _outputFilenameSuffix + ".csv";
# outputFilename = outputFilenamePrefix + _outputFilenameSuffix + ".png";
#print(matrixAsymFilename)
# print(matrixNormFilename)
# print(outputFilename)
#command = "Rscript " + heatmap_script_filename + " " + join(mat_input_dir, matrixAsymFilename) + " " + join(mat_input_dir, matrixNormFilename) + " " + join(mat_input_dir, outputFilename)
command = "Rscript " + heatmap_script_filename + " " + join(args.input_dir, matrixAsymFilename) + " " + join(args.input_dir, matrixSymFilename) + " " + join(args.output_dir, outputFilename)
command = add_metadata_args(command)
print("\t"+command)
#print command
os.system(command)# + " > /dev/null 2>&1 ")
def outputHclust(outputFilename, matrixNormFilename):
if not args.want_tree: return
command = "Rscript " + hclust_script_filename + " " + join(args.input_dir, matrixNormFilename) + " " + join(args.output_dir, outputFilename)
command = add_metadata_args(command)
print("\t"+command)
#print command
os.system(command)# + " > /dev/null 2>&1 ")
def outputPca(outputFilename, matrixNormFilename):
if not args.want_pca: return
command = "Rscript " + pca_script_filename + " " + join(args.input_dir, matrixNormFilename) + " " + join(args.output_dir, outputFilename) + " " + args.pca_axis_1 + " " + args.pca_axis_2
command = add_metadata_args(command)
print("\t"+command)
#print(args.metadata_filename)
#print(args.metadata_variable)
#print command
os.system(command)# + " > /dev/null 2>&1 ")
def execute():
files = [ f for f in listdir(args.input_dir) if isfile(join(args.input_dir,f))]
for filename in files:
asym = False
if not ".csv.gz" in filename: continue
if "asym" in filename:
asym = True
asym_filename = filename
filename = filename.replace("_asym", "")
method_name = filename.split(".")[0]
method_name = method_name.replace("mat_", "")
try:
if asym:
matrix[method_name].append(asym_filename)
else:
matrix[method_name].append(filename)
except:
matrix[method_name] = []
if asym:
matrix[method_name].append(asym_filename)
else:
matrix[method_name].append(filename)
#for method_name in matrix.keys():
#print(filename, method_name)
#if method_name in filename:
#matrix[method_name].append(filename)
#break
for method_name, matrix_filenames in matrix.items():
print("")
print(method_name)
#one version of the similairty function (sym)
if len(matrix_filenames) == 1:
#print("lala")
outputHeatmap("heatmap_" + method_name, matrix_filenames[0], matrix_filenames[0])
outputHclust("hclust_" + method_name, matrix_filenames[0])
outputPca("pca_" + method_name, matrix_filenames[0])
#two version of the similarity function (sym and asym)
else:
sym = ""
asym = ""
for filename in matrix_filenames:
if "asym" in filename:
asym = filename
else:
sym = filename
outputHeatmap("heatmap_" + method_name, asym, sym)
outputHclust("hclust_" + method_name, sym)
outputPca("pca_" + method_name, sym)
#args = sys.argv
#mat_input_dir = args[1]
#try:
# rscript_dir = args[2]
#except:
# rscript_dir = os.path.dirname(os.path.realpath(__file__))
rscript_dir = os.path.dirname(os.path.realpath(__file__))
heatmap_script_filename = join(rscript_dir, "heatmap.r")
hclust_script_filename = join(rscript_dir, "dendro.r")
pca_script_filename = join(rscript_dir, "pca.r")
if not args.want_heatmap and not args.want_pca and not args.want_tree:
print("Please, choose at least one option among: -heatmap -tree -pca")
exit(1)
if not os.path.exists(args.output_dir):
os.makedirs(args.output_dir)
execute()
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