minor edits to libraries loaded

cancersysbio · Mar 19, 2024 · c615b6a · c615b6a
1 parent 1ed05d1
commit c615b6a
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Showing 5 changed files with 7 additions and 10 deletions.
diff --git a/figures/figure2/create_figure2cd.R b/figures/figure2/create_figure2cd.R
@@ -3,13 +3,10 @@
 
 ### PREAMBLE ######################################################################################
 library(BoutrosLab.plotting.general)
-library(argparse)
-library(plyr)
-library(vcfR)
-library(bedr)
+library(tidyr)
 
 # Set the main path for repo
-main_repo_path <- ""
+main_repo_path <- "/Users/khoulaha/git/germline-epitopes"
 if ((!exists("main_repo_path")) | main_repo_path == "") {
   stop("Error: Path for main repo not set. Please set main_repo_path <- '/path/to/repo/germline-epitopes' and try again.")
 }
@@ -173,4 +170,4 @@ create.boxplot(
 	width = 6,
 	height = 7,
 	resolution = 300
-	)
+	)
diff --git a/supplementary_figures/supplementary_figure1/create_supplementary_figure1k.R b/supplementary_figures/supplementary_figure1/create_supplementary_figure1k.R
@@ -4,7 +4,7 @@
 
 ### PREAMBLE ######################################################################################
 library(BoutrosLab.plotting.general)
-library(plyr)
+library(tidyr)
 
 main_repo_path <- ""
 if ((!exists("main_repo_path")) | main_repo_path == "") {

diff --git a/supplementary_figures/supplementary_figure2/create_supplementary_figure2mn.R b/supplementary_figures/supplementary_figure2/create_supplementary_figure2mn.R
@@ -4,7 +4,7 @@
 
 ### PREAMBLE ######################################################################################
 library(BoutrosLab.plotting.general)
-library(plyr)
+library(tidyr)
 
 main_repo_path <- ""
 if ((!exists("main_repo_path")) | main_repo_path == "") {

diff --git a/supplementary_figures/supplementary_figure2/create_supplementary_figure2op.R b/supplementary_figures/supplementary_figure2/create_supplementary_figure2op.R
@@ -4,7 +4,7 @@
 
 ### PREAMBLE ######################################################################################
 library(BoutrosLab.plotting.general)
-library(plyr)
+library(tidyr)
 
 main_repo_path <- ""
 if ((!exists("main_repo_path")) | main_repo_path == "") {

diff --git a/supplementary_figures/supplementary_figure3/create_supplementary_figure3j.R b/supplementary_figures/supplementary_figure3/create_supplementary_figure3j.R
@@ -4,7 +4,7 @@
 
 ### PREAMBLE ######################################################################################
 library(BoutrosLab.plotting.general)
-library(plyr)
+library(tidyr)
 
 # Set the main path for repo
 main_repo_path <- ""