🐛 missing function and start deconvoluting utils, add imports to pkg

Author: enryH

pyproject.toml

@@ -31,11 +31,11 @@ dependencies = [
     "matplotlib",
     "kaleido",
     "pyvis",
-    # "wordcloud",
+    "wordcloud",
     "cyjupyter",
     "nltk",
-    # "webweb"
-    # "acore",
+    "webweb",
+    "acore",
     "dash-cytoscape",
 ]
 

src/vuecore/linkers.py

@@ -0,0 +1,20 @@
+from io import StringIO
+
+import requests
+
+
+def get_clustergrammer_link(net, filename=None):
+    clustergrammer_url = "http://amp.pharm.mssm.edu/clustergrammer/matrix_upload/"
+    if filename is None:
+        file_string = net.write_matrix_to_tsv()
+        file_obj = StringIO(file_string)
+        if "filename" not in net.dat or net.dat["filename"] is None:
+            fake_filename = "Network.txt"
+        else:
+            fake_filename = net.dat["filename"]
+        r = requests.post(clustergrammer_url, files={"file": (fake_filename, file_obj)})
+    else:
+        file_obj = open(filename, "r")
+        r = requests.post(clustergrammer_url, files={"file": file_obj})
+    link = r.text
+    return link

src/vuecore/translate.py

@@ -0,0 +1,20 @@
+import base64
+import io
+
+from dash import html
+
+
+def hex2rgb(color):
+    _hex = color.lstrip("#")
+    rgb = tuple(int(_hex[i : i + 2], 16) for i in (0, 2, 4))
+    rgba = rgb + (0.6,)
+    return rgba
+
+
+def mpl_to_html_image(plot, width=800):
+    buf = io.BytesIO()
+    plot.savefig(buf, format="png")
+    data = base64.b64encode(buf.getbuffer()).decode("utf8")
+    figure = html.Img(src="data:image/png;base64,{}".format(data), width=f"{width}")
+
+    return figure

src/vuecore/utils.py

@@ -1,11 +1,8 @@
-import base64
-import io
 import random
 from collections import defaultdict
 from urllib import error
 
 import bs4 as bs
-import dash_html_components as html
 import networkx as nx
 import pandas as pd
 import requests
@@ -24,15 +21,6 @@ def check_columns(df, cols):
     return True
 
 
-def mpl_to_html_image(plot, width=800):
-    buf = io.BytesIO()
-    plot.savefig(buf, format="png")
-    data = base64.b64encode(buf.getbuffer()).decode("utf8")
-    figure = html.Img(src="data:image/png;base64,{}".format(data), width="800")
-
-    return figure
-
-
 def generate_html(network):
     """
     This method gets the data structures supporting the nodes, edges,
@@ -282,13 +270,6 @@ def __extract_style(el):
         return getattr(html, name.title())(contents, style=style)
 
 
-def hex2rgb(color):
-    hex = color.lstrip("#")
-    rgb = tuple(int(hex[i : i + 2], 16) for i in (0, 2, 4))
-    rgba = rgb + (0.6,)
-    return rgba
-
-
 def get_rgb_colors(n):
     colors = []
     r = int(random.random() * 256)

src/vuecore/viz.py

@@ -31,7 +31,9 @@
 from webweb import Web
 from wordcloud import STOPWORDS, WordCloud
 
-from . import dendrogram, utils, wgcna
+from . import utils
+from .linkers import get_clustergrammer_link
+from .translate import hex2rgb, mpl_to_html_image
 
 # matplotlib.use("Agg")
 
@@ -2128,7 +2130,7 @@ def get_sankey_plot(
                 label=nodes,
                 color=[
                     (
-                        "rgba" + str(utils.hex2rgb(node_colors[c]))
+                        "rgba" + str(hex2rgb(node_colors[c]))
                         if node_colors[c].startswith("#")
                         else node_colors[c]
                     )
@@ -2140,7 +2142,7 @@ def get_sankey_plot(
                 target=[list(nodes).index(i) for i in data[args["target"]].tolist()],
                 value=data[args["weight"]].tolist(),
                 color=[
-                    "rgba" + str(utils.hex2rgb(c)) if c.startswith("#") else c
+                    "rgba" + str(hex2rgb(c)) if c.startswith("#") else c
                     for c in data[args["source_colors"]].tolist()
                 ],
                 label=hover_data,
@@ -2413,7 +2415,7 @@ def get_clustergrammer_plot(data, identifier, args):
                 )
         clustergrammer_net.load_df(data)
 
-        link = utils.get_clustergrammer_link(clustergrammer_net, filename=None)
+        link = get_clustergrammer_link(clustergrammer_net, filename=None)
 
         iframe = html.Iframe(src=link, width=1000, height=900)
 
@@ -2547,7 +2549,7 @@ def get_WGCNAPlots(data, identifier):
                 height=800,
             )
         )
-        dendro_tree = wgcnaAnalysis.get_dendrogram(
+        dendro_tree = wgcna_analysis.get_dendrogram(
             METDiss, METDiss.index, distfun=None, linkagefun="ward", div_clusters=False
         )
         if dendro_tree is not None:
@@ -2611,12 +2613,12 @@ def get_WGCNAPlots(data, identifier):
                     )
                 )
             ):
-                df = wgcnaAnalysis.get_percentiles_heatmap(
+                df = wgcna_analysis.get_percentiles_heatmap(
                     METcor, dendro_tree, bydendro=True, bycols=False
                 ).T
             else:
-                df = wgcnaAnalysis.df_sort_by_dendrogram(
-                    wgcnaAnalysis.df_sort_by_dendrogram(METcor, dendro_tree).T,
+                df = wgcna_analysis.df_sort_by_dendrogram(
+                    wgcna_analysis.df_sort_by_dendrogram(METcor, dendro_tree).T,
                     dendro_tree,
                 )
 
@@ -3271,7 +3273,7 @@ def get_km_plot(data, identifier, args):
             plot.set_xlabel(xlabel)
             plot.set_ylabel(ylabel)
             if environment == "app":
-                figure = utils.mpl_to_html_image(plot.figure, width=800)
+                figure = mpl_to_html_image(plot.figure, width=800)
                 result = html.Div(id=identifier, children=[figure])
             else:
                 result = plot.figure
@@ -3311,7 +3313,7 @@ def get_cumulative_hazard_plot(data, identifier, args):
             plot.set_xlabel(xlabel)
             plot.set_ylabel(ylabel)
             if environment == "app":
-                figure = utils.mpl_to_html_image(plot.figure, width=800)
+                figure = mpl_to_html_image(plot.figure, width=800)
                 result = html.Div(id=identifier, children=[figure])
             else:
                 result = plot.figure