Skip to content

Commit

Permalink
fixed some errors
Browse files Browse the repository at this point in the history
  • Loading branch information
@julenmendieta
julenmendieta committed Sep 7, 2021
1 parent 74fc9db commit 5c10f6e
Showing 1 changed file with 48 additions and 26 deletions.
74 changes: 48 additions & 26 deletions bioinfokit/visuz.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -261,7 +261,6 @@ def ma(df="dataframe", lfc=None, ct_count=None, st_count=None, lfc_thr=(1, 1), v
# this is important to check if color or A exists and drop them as if you run multiple times same command
# it may update old instance of df
df = df.drop(['color_add_axy', 'A_add_axy'], axis=1, errors='ignore')
assert len(set(color)) == 3, 'unique color must be size of 3'
if noiseFilter == False:
df.loc[(df[lfc] >= lfc_thr[0]), 'color_add_axy'] = color[0] # upregulated
df.loc[(df[lfc] <= -lfc_thr[1]), 'color_add_axy'] = color[2] # downregulated
Expand All @@ -285,38 +284,34 @@ def ma(df="dataframe", lfc=None, ct_count=None, st_count=None, lfc_thr=(1, 1), v
# set(color_result_num)) == 3, 'either significant or non-significant genes are missing; try to change lfc_thr' \
# ' to include both significant and non-significant genes'
originalColor = color
if len(set(color_result_num)) != 3:
if not 0 in color_result_num:
color = color[1:]
if not 2 in color_result_num:
color = color[0]
if theme:
General.style_bg(theme)
# get density values if asked
if noiseFilter != False:
pos_i = df['color_add_axy'] == originalColor[1]
# above and bellow Thress
if 0 in color_result_num:
color0 = originalColor[0]
if 2 in color_result_num:
color2 = originalColor[2]
else:
color2 = 'nomatch'
else:
color0 = 'nomatch'
if 2 in color_result_num:
color2 = originalColor[1]
else:
color2 = 'nomatch'
pos_u = df['color_add_axy'] == color0
pos_d = df['color_add_axy'] == color2
if density:
# intermediate
if noiseFilter == False:
xy_i = np.vstack([df['A_add_axy'],df[lfc]])
z_i = gaussian_kde(xy_i)(xy_i)
else:
pos_i = df['color_add_axy'] == originalColor[1]
xy_i = np.vstack([df.loc[pos_i, 'A_add_axy'],df.loc[pos_i, lfc]])
z_i = gaussian_kde(xy_i)(xy_i)
# above and bellow Thress
if 0 in color_result_num:
color0 = color[0]
if 2 in color_result_num:
color2 = color[2]
else:
color2 = 'nomatch'
else:
color0 = 'nomatch'
if 2 in color_result_num:
color2 = color[1]
else:
color2 = 'nomatch'
pos_u = df['color_add_axy'] == color0
pos_d = df['color_add_axy'] == color2

fig, ax = plt.subplots(figsize=dim)
if plotlegend:
Expand All @@ -340,8 +335,21 @@ def ma(df="dataframe", lfc=None, ct_count=None, st_count=None, lfc_thr=(1, 1), v
alpha=valpha, s=dotsize, marker=markerdot)

else:
s = plt.scatter(df['A_add_axy'], df[lfc], c=color_result_num, cmap=ListedColormap(color),
alpha=valpha, s=dotsize, marker=markerdot)
if noiseFilter == False:
s = plt.scatter(df['A_add_axy'], df[lfc], c=color_result_num, cmap=ListedColormap(color),
alpha=valpha, s=dotsize, marker=markerdot)
else:
# intermediate
s = plt.scatter(df.loc[pos_i, 'A_add_axy'], df.loc[pos_i, lfc], alpha=valpha,
s=dotsize, marker=markerdot, c=originalColor[1])
# upregulated
if color0 != 'nomatch':
s = plt.scatter(df.loc[pos_u, 'A_add_axy'], df.loc[pos_u, lfc], c=color0,
alpha=valpha, s=dotsize, marker=markerdot)
# downregulated
if color2 != 'nomatch':
s = plt.scatter(df.loc[pos_d, 'A_add_axy'], df.loc[pos_d, lfc], c=color2,
alpha=valpha, s=dotsize, marker=markerdot)
assert len(legendlabels) == 3, 'legendlabels must be size of 3'
if noiseFilter == False:
plt.legend(handles=s.legend_elements()[0], labels=legendlabels, loc=legendpos,
Expand All @@ -367,8 +375,22 @@ def ma(df="dataframe", lfc=None, ct_count=None, st_count=None, lfc_thr=(1, 1), v
alpha=valpha, s=dotsize, marker=markerdot)

else:
plt.scatter(df['A_add_axy'], df[lfc], c=color_result_num, cmap=ListedColormap(color),
alpha=valpha, s=dotsize, marker=markerdot)
if noiseFilter == False:
plt.scatter(df['A_add_axy'], df[lfc], c=color_result_num, cmap=ListedColormap(color),
alpha=valpha, s=dotsize, marker=markerdot)
else:
# intermediate
s = plt.scatter(df.loc[pos_i, 'A_add_axy'], df.loc[pos_i, lfc], alpha=valpha,
s=dotsize, marker=markerdot, c=originalColor[1])
# upregulated
if color0 != 'nomatch':
s = plt.scatter(df.loc[pos_u, 'A_add_axy'], df.loc[pos_u, lfc], c=color0,
alpha=valpha, s=dotsize, marker=markerdot)
# downregulated
if color2 != 'nomatch':
s = plt.scatter(df.loc[pos_d, 'A_add_axy'], df.loc[pos_d, lfc], c=color2,
alpha=valpha, s=dotsize, marker=markerdot)

# draw a central line at M=0
plt.axhline(y=0, color='#7d7d7d', linestyle='--')
# draw lfc threshold lines
Expand Down

0 comments on commit 5c10f6e

Please sign in to comment.