brain: add python and R code to local repository.

1 files changed, 273 insertions, 0 deletions

diff --git a/Code/make_graphviz_file3C.py b/Code/make_graphviz_file3C.py
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+# Usage: python make_graphviz_file3C.py AT1G19850

+#

+#        Make plot: python make_graphviz_file3C.py AT1G65480 | sfdp -Goverlap=false -Tpdf -o result.flower.pdf result.flower.gv

+#                   unflatten -f -l 3 result.flower.gv | dot -Tsvg -o result.flower.svg 

+#

+# Purpose: Generate result.txt for Graphviz software dot. The single

+# parameter AT1G19850 is a TF.

+# The query neighbours of the TF's neighbours are also shown.

+#

+# Created 10 July 2017, hui, slcu

+

+import random

+import numpy as np

+import sys

+from geneid2name import make_gene_name_AGI_map_dict, get_gene_name

+

+PERCENT = 1

+NUM_TARGETS_CUTOFF = 5

+

+def get_tf_tissue(fname):

+    d = {}

+    f = open(fname)

+    lines = f.readlines()

+    f.close()

+    head = lines[0].strip()

+    head_lst = head.split('\t')

+    head_lst = head_lst[1:] # remove TF

+    for line in lines[1:]:

+        line = line.strip()

+        lst = line.split('\t')

+        lst2 = lst[1:]

+        lst3 = [int(x) for x in lst2]

+        lst4 = np.array(lst3)

+        median_val = np.median(lst4)

+        tissue = []

+        for i in range(len(lst2)):

+            if int(lst2[i]) >= max(median_val, 1) or int(lst2[i]) >= NUM_TARGETS_CUTOFF:

+                tissue.append(head_lst[i])

+        tf = (lst[0].split())[0]

+        d[tf] = tissue # tf is assigned with a list of tissues, the tissue with node degree greater than median are selected.

+    return d

+

+

+def get_tissue_from_fname(fname):

+    tissue_lst = [

+        'seedling',

+        'meristem',

+        'flower',

+        'aerial',

+        'shoot',

+        'seed',

+        'leaf',

+        'root',

+        'stem']

+    for x in tissue_lst:

+        if x in fname:

+            return x

+    return 'unknown'

+

+

+def get_edge(fname):

+    ''' Return d = {'flower':{'tf':[target1,target2, ...]}, 'seed':{}} '''

+    d = {}

+    d2 = {} # the actual correlation coefficient, absolute value

+    f = open(fname)

+    for line in f:

+        line = line.strip()

+        if not line.startswith('#'):

+            lst = line.split('\t')

+            target = (lst[0].split('_'))[0]

+            tf     = (lst[1].split('_'))[0]

+            if not tf in d[tissue]:

+                d[tissue][tf] = [target]

+            else:

+                d[tissue][tf].append(target)

+

+            strength = abs(float(lst[2]))

+            if not tf in d2[tissue]:

+                d2[tissue][tf] = {target:strength}

+            else:

+                d2[tissue][tf][target] = strength

+                

+        else:

+            tissue = get_tissue_from_fname(line)

+            d[tissue] = {}

+            d2[tissue] = {}            

+    f.close()

+    return d, d2

+

+

+def in_same_tissue(source, target, node_dict):

+    return node_dict[source] == node_dict[target]

+

+

+def make_label(a, b):

+    if b == '.':

+        return a

+    else:

+        lst = b.split(';')

+        return a + '_' + lst[0]

+

+

+def has_predecessor(tf, d):

+    for k in d:

+        if tf in d[k] and k != tf:

+            return True

+    return False

+

+def get_num_successors(tf, d):

+    if not tf in d:

+        return 0

+    return len(d[tf])

+

+def get_shape(tf, d):

+    ''' d = {'tf':[target1, target2]} '''

+    p = has_predecessor(tf, d)

+    s = get_num_successors(tf, d)

+    if s > 0 and p:

+        return 'doublecircle'

+    if s > 0:

+        return 'ellipse' # regulator

+    if p:

+        return 'egg' # regulatee

+

+

+def get_color(tf, edge_dict, tissue):

+    #colours = ['darkolivegreen1', 'darkolivegreen2', 'darkolivegreen3', 'darkolivegreen4', 'gold', 'gold1', 'gold2', 'gold3', 'gold4', 'darkgoldenrod', 'darkgoldenrod4']

+    #colours = ['snow', 'snow1', 'snow2', 'snow3', 'snow4', 'gold', 'gold1', 'gold2', 'gold3', 'gold4']

+    colours = ['springgreen', 'springgreen1', 'springgreen2', 'springgreen3', 'springgreen4', 'gold', 'gold1', 'gold2', 'gold3', 'gold4']

+    d = {}

+    total = 0

+    for k in edge_dict:

+        n = get_num_successors(tf, edge_dict[k])

+        d[k] = n

+        total += n

+        #print('%s %d' % (k, n))

+    if total == 0:

+        return 'azure'

+    return colours[min(int(10 * 1.0 * d[tissue] / total), len(colours)-1)]

+

+

+def make_more_string(n, tissue, edge_dict, colour_dict, agi2name_dict, query_tf):

+    result = ''

+    d = edge_dict[tissue]

+    if n in d:

+        for target in d[n]:

+            ll = make_label(target, get_gene_name(target, agi2name_dict))

+            shape = get_shape(target, d)

+            color = get_color(target, edge_dict, tissue)

+            node_target = target + '_' + tissue + '.2'

+            if target != query_tf:

+                result += '     \"%s\" [label=\"%s\", fillcolor=%s, color=%s, shape=%s, style=filled];\n' % (node_target, ll, color, colour_dict[tissue], shape)

+

+                node_n = n + '_' + tissue

+                if random.uniform(0, 1) <= PERCENT:

+                    result += '     \"%s\" -> \"%s\" [color=%s];\n' % (node_n, node_target, 'gold')

+

+    for tf in d:

+        if tf != query_tf:

+            if n in d[tf]: # n is successor

+                ll = make_label(tf, get_gene_name(tf, agi2name_dict))

+                shape = get_shape(tf, d)

+                color = get_color(tf, edge_dict, tissue)

+                node_tf = tf + '_' + tissue + '.2'

+                result += '     \"%s\" [label=\"%s\", fillcolor=%s, color=%s, shape=%s, style=filled];\n' % (node_tf, ll, color, colour_dict[tissue], shape)

+

+                node_n = n + '_' + tissue

+                if random.uniform(0, 1) <= PERCENT:

+                    result += '     \"%s\" -> \"%s\" [color=%s];\n' % (node_tf, node_n, 'red')

+

+    return result

+

+

+def write_graphviz_file(fname, edge_dict, colour_dict, agi2name_dict, query_tf):

+

+    f = open(fname, 'w')

+    

+    graph_dict = {}

+    more = {}

+    for k in edge_dict:

+        graph_dict[k] = {'head':'', 'nodes':[], 'edges':[]}

+

+    for k in edge_dict: # k is tissue

+        neighbours = []

+        node_added_dict = {}

+        tissue_node = '%s_node' % (k)

+        graph_dict[k]['head'] = ''

+        d = edge_dict[k]

+        tf_lst = d.keys()

+        for tf in tf_lst:

+            node_tf = tf + '_' + k            

+            if tf == query_tf:

+                ll = make_label(tf, get_gene_name(tf, agi2name_dict))

+                shape = get_shape(tf, d)

+                color = get_color(tf, edge_dict, k)

+                if not tf in node_added_dict:

+                    graph_dict[k]['nodes'].append('     \"%s\" [label=\"%s\", fillcolor=%s, color=%s, shape=%s, style=filled];\n' % (node_tf, 'Query gene: '+ll, 'DeepSkyBlue', colour_dict[k], shape))

+                    node_added_dict[tf] = 'YES'

+                for target in d[tf]:

+                    ll = make_label(target, get_gene_name(target, agi2name_dict))

+                    node_target = target + '_' + k

+                    shape = get_shape(target, d)

+                    color = get_color(target, edge_dict, k)

+                    if random.uniform(0, 1) <= PERCENT:

+                        if not target in node_added_dict:

+                            neighbours.append(target)

+                            graph_dict[k]['nodes'].append('     \"%s\" [label=\"%s\", fillcolor=%s, color=%s, shape=%s, style=filled];\n' % (node_target, ll, color, colour_dict[k], shape))

+                            node_added_dict[target] = 'YES'

+                            graph_dict[k]['edges'].append('     \"%s\" -> \"%s\" [color=%s];\n' % (node_tf, node_target, 'gold'))

+            else: # check if tf is a target of another tf

+                for target in d[tf]:

+                    if target == query_tf:

+                        ll = make_label(tf, get_gene_name(tf, agi2name_dict))

+                        node_tf = tf + '_' + k

+                        shape = get_shape(tf, d)

+                        color = get_color(tf, edge_dict, k)

+                        node_target = target + '_' + k

+                        if random.uniform(0, 1) <= PERCENT:

+                            if not tf in node_added_dict:

+                                neighbours.append(tf)                                

+                                graph_dict[k]['nodes'].append('     \"%s\" [label=\"%s\", fillcolor=%s, color=%s, shape=%s, style=filled];\n' % (node_tf, ll, color, colour_dict[k], shape))

+                                node_added_dict[tf] = 'YES'

+                            graph_dict[k]['edges'].append('     \"%s\" -> \"%s\" [color=%s];\n' % (node_tf, node_target, 'red'))

+        neighbours = list(set(neighbours))

+        more[k] = ''

+        for n in neighbours:

+            more[k] += make_more_string(n, k, edge_dict, colour_dict, agi2name_dict, query_tf)

+            

+

+    for k in graph_dict:

+        if graph_dict[k]['nodes'] != []:

+            f = open(fname + '.' +  k + '.gv', 'w')

+            s0 = 'digraph G {\n    graph[splines=true, ranksep=3, fontname=Arial];\n    node[fontname=Arial];\n'

+            s0 += graph_dict[k]['head']

+            for x in graph_dict[k]['nodes']:

+                s0 += x

+            for x in graph_dict[k]['edges']:

+                s0 += x

+            if k in more:

+                s0 += more[k]

+            s0 += '}\n'

+            f.write(s0)        

+            f.close()

+

+# main

+

+GENE_ID_TO_GENE_NAME    = '../Data/information/AGI-to-gene-names_v2.txt'

+agi2name_dict = make_gene_name_AGI_map_dict(GENE_ID_TO_GENE_NAME)

+

+edge_file = 'result.skeleton.txt'  # prepared by test_network4.py

+node_file = 'result.out.txt'       # prepared by test_network4.py

+

+tissue_colour_dict = {

+        'seedling':'greenyellow',

+        'meristem':'skyblue4',

+        'flower':'lightpink',

+        'aerial':'cyan',

+        'shoot':'forestgreen',

+        'seed':'black',

+        'leaf':'green',

+        'root':'gold',

+        'stem':'orange4'}

+

+

+

+if len(sys.argv) < 2:

+    sys.exit()

+else:

+    query_tf = sys.argv[1]

+    

+#tf_tissue_dict = get_tf_tissue(node_file )

+edge_dict, edge_dict_r = get_edge(edge_file)

+write_graphviz_file('result', edge_dict, tissue_colour_dict, agi2name_dict, query_tf)