Mercurial > repos > azomics > clustergrammer_flow

comparison clustergrammerIPG.py @ 1:c90127c2a1ae draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit e47edffe14c2e8544fe0d00d932090657beae528"
author azomics
date Sun, 27 Jun 2021 22:13:16 +0000
parents fee56ee2f7ac
children
comparison
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0:fee56ee2f7ac 1:c90127c2a1ae
11 # version 1.2 -- June 2018 11 # version 1.2 -- June 2018
12 # added clustergrammer clustering parameters and normalization options 12 # added clustergrammer clustering parameters and normalization options
13 13
14 14
15 from __future__ import print_function 15 from __future__ import print_function
16
17 import os
16 import sys 18 import sys
17 import os 19
20 from clustergrammer import Network
18 21
19 from jinja2 import Environment, FileSystemLoader 22 from jinja2 import Environment, FileSystemLoader
23
20 import pandas as pd 24 import pandas as pd
21 from clustergrammer import Network
22 25
23 26
24 def is_integer(s): 27 def is_integer(s):
25 try: 28 try:
26 int(s) 29 int(s)
50 else: 53 else:
51 output_list.append(int(tmp_col[c].strip()) - 1) 54 output_list.append(int(tmp_col[c].strip()) - 1)
52 return(output_list) 55 return(output_list)
53 56
54 57
55 def prepare_heatmap(matrix_input, html_file, html_dir, tools_dir, categories, distance, linkage): 58 def prepare_heatmap(matrix_input, html_file, html_dir, tools_dir,
59 categories, distance, linkage):
56 # prepare directory and html 60 # prepare directory and html
57 os.mkdir(html_dir) 61 os.mkdir(html_dir)
58 62
59 env = Environment(loader=FileSystemLoader(tools_dir + "/templates")) 63 env = Environment(loader=FileSystemLoader(tools_dir + "/templates"))
60 template = env.get_template("clustergrammer.template") 64 template = env.get_template("clustergrammer.template")
89 'row': df.iloc[:, 0], 93 'row': df.iloc[:, 0],
90 'col': df.columns[1:] 94 'col': df.columns[1:]
91 } 95 }
92 96
93 tmp_string = "-=-".join(args[8:]) 97 tmp_string = "-=-".join(args[8:])
94 print (tmp_string + "\n") 98 print(tmp_string + "\n")
95 # get categories 99 # get categories
96 cats = tmp_string.split("-=-new_cat-=-") 100 cats = tmp_string.split("-=-new_cat-=-")
97 for cat in cats: 101 for cat in cats:
98 tmp_cat = cat.split("-=-") 102 tmp_cat = cat.split("-=-")
99 group = { 103 group = {
116 print(index_names, elem[0], sep="\t") 120 print(index_names, elem[0], sep="\t")
117 group["cats"][elem[0]] = index_names 121 group["cats"][elem[0]] = index_names
118 categories[tmp_cat[0]].append(group) 122 categories[tmp_cat[0]].append(group)
119 print(categories) 123 print(categories)
120 124
121 125 prepare_heatmap(args[1], args[2], args[3],
122 prepare_heatmap(args[1], args[2], args[3], args[4], categories, args[5], args[6]) 126 args[4], categories, args[5], args[6])