Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

added code for sup fig 6 #2

Open
wants to merge 2 commits into
base: master
Choose a base branch
from
Open

added code for sup fig 6 #2

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
c72a763
added code for sup fig 6
tatet2 Jan 28, 2022
f348f89
saved fig sup6 as pdf
tatet2 Jan 28, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
0 figures/indivbrca_data_noids.csv → data/indivbrca_data_noids.csv
View file
Open in desktop
File renamed without changes.
474,518 changes: 474,518 additions & 0 deletions data/sup6data.csv
View file
Open in desktop

Large diffs are not rendered by default.

2 changes: 1 addition & 1 deletion figures/Fig2a.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ library(ggplot2)

## embryo simulation results

emb <- fread("./indivbrca_data_noids.csv")
emb <- fread("./data/indivbrca_data_noids.csv")

## with original beta

Expand Down
35 changes: 35 additions & 0 deletions figures/SuppFigure6.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,35 @@
#!/usr/env python


import os
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt


datapath = os.path.abspath(os.path.join(os.path.dirname(__file__), '../data'))
figpath = os.path.abspath(os.path.dirname(__file__))

popdata = pd.read_csv(os.path.join(datapath, 'sup6data.csv'))


fig, axs = plt.subplots(ncols=2, sharey=False)

sns.kdeplot(popdata['PGS000008_breast_cancer_score'].loc[popdata.population == 'EUR'], ax=axs[0], legend=False)
sns.kdeplot(popdata['PGS000008_breast_cancer_score'].loc[popdata.population == 'AFR'], ax=axs[0], legend=False)
sns.kdeplot(popdata['PGS000008_breast_cancer_score'].loc[popdata.population == 'SAS'], ax=axs[0], legend=False)
sns.kdeplot(popdata['PGS000008_breast_cancer_score'].loc[popdata.population == 'EAS'], ax=axs[0], legend=False)
sns.kdeplot(popdata['PGS000008_breast_cancer_score'].loc[popdata.population == 'AKJ'], ax=axs[0], legend=False)
axs[0].set(xlabel="raw score")

sns.kdeplot(popdata['standardized'].loc[popdata.population == 'AFR'], ax=axs[1], legend=False)
sns.kdeplot(popdata['standardized'].loc[popdata.population == 'EUR'], ax=axs[1], legend=False)
sns.kdeplot(popdata['standardized'].loc[popdata.population == 'SAS'], ax=axs[1], legend=False)
sns.kdeplot(popdata['standardized'].loc[popdata.population == 'EAS'], ax=axs[1], legend=False)
sns.kdeplot(popdata['zscore'].loc[popdata.population == 'AKJ'], ax=axs[1], legend=False)
axs[1].set(xlabel="corrected score")
axs[1].set(ylabel=None)

plt.legend(title=None, labels=['EUR', 'AFR', 'SAS', 'EAS', 'AKJ'])

fig.savefig(os.path.join(figpath, 'sup6.pdf'))
35 changes: 35 additions & 0 deletions figures/SuppFigure6.py~
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,35 @@
#!/usr/env python


import os
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt


datapath = os.path.abspath(os.path.join(os.path.dirname(__file__), '../data'))

popdata = pd.read_csv(os.path.join(datapath, 'sup6data.csv'))


fig, axs = plt.subplots(ncols=2, sharey=False)

sns.kdeplot(popdata['PGS000008_breast_cancer_score'].loc[popdata.population == 'EUR'], ax=axs[0], legend=False)
sns.kdeplot(popdata['PGS000008_breast_cancer_score'].loc[popdata.population == 'AFR'], ax=axs[0], legend=False)
sns.kdeplot(popdata['PGS000008_breast_cancer_score'].loc[popdata.population == 'SAS'], ax=axs[0], legend=False)
sns.kdeplot(popdata['PGS000008_breast_cancer_score'].loc[popdata.population == 'EAS'], ax=axs[0], legend=False)
sns.kdeplot(popdata['PGS000008_breast_cancer_score'].loc[popdata.population == 'AKJ'], ax=axs[0], legend=False)
axs[0].set(xlabel="raw score")

sns.kdeplot(popdata['standardized'].loc[popdata.population == 'AFR'], ax=axs[1], legend=False)
sns.kdeplot(popdata['standardized'].loc[popdata.population == 'EUR'], ax=axs[1], legend=False)
sns.kdeplot(popdata['standardized'].loc[popdata.population == 'SAS'], ax=axs[1], legend=False)
sns.kdeplot(popdata['standardized'].loc[popdata.population == 'EAS'], ax=axs[1], legend=False)
sns.kdeplot(popdata['zscore'].loc[popdata.population == 'AKJ'], ax=axs[1], legend=False)
axs[1].set(xlabel="corrected score")
axs[1].set(ylabel=None)

plt.legend(title=None, labels=['EUR', 'AFR', 'SAS', 'EAS', 'AKJ'])

fig.savefig('sup6.png')

Binary file added figures/sup6.pdf
View file
Open in desktop
Binary file not shown.
Binary file added figures/sup6.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.