Merge pull request #2 from StatFunGen/main

update from main

Author: xueweic

.DS_Store

@@ -0,0 +1,33 @@
+name: deploy-book
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  deploy-book:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.9
+
+    - name: Install dependencies
+      run: |
+        pip install jupyter-book
+        pip install ghp-import
+
+    - name: Build the book
+      run: |
+        jupyter-book build . --config manuscript-website/_config.yml --toc manuscript-website/_toc.yml
+
+    - name: GitHub Pages action
+      uses: peaceiris/actions-gh-pages@v3.6.1
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ./_build/html
+

.github/workflows/deploy-book.yml

@@ -47,3 +47,34 @@ po/*~
 
 # RStudio Connect folder
 rsconnect/
+
+# Jupyter Notebook specific
+.ipynb_checkpoints
+*/.ipynb_checkpoints/*
+*.nbconvert.ipynb
+.jupyter/
+jupyter_notebook_config.py
+
+# Mac specific
+.DS_Store
+.AppleDouble
+.LSOverride
+Icon
+._*
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Editor specific files
+.idea/
+.vscode/
+*.swp
+*.swo
+*~
+
+# Jupyter Book
+_build

.gitignore

@@ -22,7 +22,7 @@
     "library(ggpattern)\n",
     "library(ggpubr)\n",
     "library(cowplot)\n",
-    "sumstat <- readRDS(\"Figure2a.rds\")\n",
+    "sumstat <- readRDS(\"Figure_2a.rds\")\n",
     "sumstat <- sumstat %>% filter(max_causal != 4)\n",
     "colors_man <- c(\"#B24745FF\", \"#00A1D5FF\", \"#79AF97FF\", \"#DF8F44FF\")"
    ]

Main Figures/.DS_Store Main_Figures/.DS_StoreMain Figures/.DS_Store renamed to Main_Figures/.DS_Store

@@ -69,7 +69,7 @@
    ],
    "source": [
     "library(tidyverse)\n",
-    "data <- readRDS(\"Figure2b.rds\")$HeterogeneousEffect\n",
+    "data <- readRDS(\"Figure_2b.rds\")$HeterogeneousEffect\n",
     "X <- data$X\n",
     "Y <- data$Y\n",
     "data$variant"
@@ -1179,7 +1179,7 @@
    ],
    "source": [
     "library(tidyverse)\n",
-    "data <- readRDS(\"Figure2b.rds\")$LDInfluence\n",
+    "data <- readRDS(\"Figure_2b.rds\")$LDInfluence\n",
     "X <- data$X\n",
     "Y <- data$Y\n",
     "data$variant"
@@ -2052,7 +2052,7 @@
    ],
    "source": [
     "library(tidyverse)\n",
-    "data <- readRDS(\"Figure2b.rds\")$WeakerTarget\n",
+    "data <- readRDS(\"Figure_2b.rds\")$WeakerTarget\n",
     "X <- data$X\n",
     "Y <- data$Y\n",
     "data$variant"

Main Figures/Figure2/.DS_Store Main_Figures/Figure_2/.DS_StoreMain Figures/Figure2/.DS_Store renamed to Main_Figures/Figure_2/.DS_Store

@@ -22,7 +22,7 @@
     "library(ggpattern)\n",
     "library(ggpubr)\n",
     "library(cowplot)\n",
-    "res <- readRDS(\"Figure2c.rds\")\n",
+    "res <- readRDS(\"Figure_2c.rds\")\n",
     "colors_man <- c(\"#B24745FF\", \"#00A1D5FF\", \"#79AF97FF\", \"#DF8F44FF\")"
    ]
   },

…nb_checkpoints/Figure2a-checkpoint.ipynb …nb_checkpoints/Figure2a-checkpoint.ipynbMain Figures/Figure2/.ipynb_checkpoints/Figure2a-checkpoint.ipynb renamed to Main_Figures/Figure_2/.ipynb_checkpoints/Figure2a-checkpoint.ipynb Main Figures/Figure2/.ipynb_checkpoints/Figure2a-checkpoint.ipynb renamed to Main_Figures/Figure_2/.ipynb_checkpoints/Figure2a-checkpoint.ipynb

@@ -22,7 +22,7 @@
     "library(ggpattern)\n",
     "library(ggpubr)\n",
     "library(cowplot)\n",
-    "sumstat <- readRDS(\"Figure2d.rds\")\n",
+    "sumstat <- readRDS(\"Figure_2d.rds\")\n",
     "sumstat <- sumstat %>% filter(heritability != 0.05)\n",
     "colors_man <- c(\"#B24745FF\", \"#00A1D5FF\", \"#79AF97FF\", \"#DF8F44FF\")"
    ]

…nb_checkpoints/Figure2b-checkpoint.ipynb …nb_checkpoints/Figure2b-checkpoint.ipynbMain Figures/Figure2/.ipynb_checkpoints/Figure2b-checkpoint.ipynb renamed to Main_Figures/Figure_2/.ipynb_checkpoints/Figure2b-checkpoint.ipynb Main Figures/Figure2/.ipynb_checkpoints/Figure2b-checkpoint.ipynb renamed to Main_Figures/Figure_2/.ipynb_checkpoints/Figure2b-checkpoint.ipynb

@@ -22,7 +22,7 @@
     "library(ggpattern)\n",
     "library(ggpubr)\n",
     "library(cowplot)\n",
-    "result <- readRDS(\"Figure2e.rds\")\n",
+    "result <- readRDS(\"Figure_2e.rds\")\n",
     "result$method <- factor(result$method, levels = c(\"ColocBoost\", \"OPERA\"))\n",
     "colors_man <- c(\"#B24745FF\", \"#1d4a9e\")"
    ]