Make R library imports consistent with Mike style

ruppinlab · Aug 19, 2021 · d9b8d48 · d9b8d48
1 parent 86694cf
commit d9b8d48
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Showing 7 changed files with 44 additions and 34 deletions.
diff --git a/count_eset_case_info.R b/count_eset_case_info.R
@@ -1,4 +1,4 @@
-suppressPackageStartupMessages(library("Biobase"))
+suppressPackageStartupMessages(library(Biobase))
 
 uniq_kraken_case_uuids <- c()
 uniq_kraken_na_case_uuids <- c()

diff --git a/create_esets.R b/create_esets.R
@@ -1,9 +1,11 @@
 options(warn=1)
-suppressPackageStartupMessages(library("argparser"))
-suppressPackageStartupMessages(library("Biobase"))
-suppressPackageStartupMessages(library("data.table"))
-suppressPackageStartupMessages(library("GenomicDataCommons"))
-suppressPackageStartupMessages(library("stringr"))
+suppressPackageStartupMessages({
+    library(argparser)
+    library(Biobase)
+    library(data.table)
+    library(GenomicDataCommons)
+    library(stringr)
+})
 
 stopifnot(GenomicDataCommons::status()$status == "OK")
 

diff --git a/generate_violin_plots.R b/generate_violin_plots.R
@@ -1,13 +1,15 @@
 options(warn=1)
-suppressPackageStartupMessages(library("argparser"))
-suppressPackageStartupMessages(library("dplyr"))
-suppressPackageStartupMessages(library("gdtools"))
-suppressPackageStartupMessages(library("ggplot2"))
-suppressPackageStartupMessages(library("ggsignif"))
-suppressPackageStartupMessages(library("ggstatsplot"))
-suppressPackageStartupMessages(library("ggtext"))
-suppressPackageStartupMessages(library("pairwiseComparisons"))
-suppressPackageStartupMessages(library("stringr"))
+suppressPackageStartupMessages({
+    library(argparser)
+    library(dplyr)
+    library(gdtools)
+    library(ggplot2)
+    library(ggsignif)
+    library(ggstatsplot)
+    library(ggtext)
+    library(pairwiseComparisons)
+    library(stringr)
+})
 
 set.seed(777)
 

diff --git a/get_gtf_ensg_annots.R b/get_gtf_ensg_annots.R
@@ -1,10 +1,12 @@
-suppressPackageStartupMessages(library("AnnotationHub"))
-suppressPackageStartupMessages(library("argparser"))
-suppressPackageStartupMessages(library("ensembldb"))
-suppressPackageStartupMessages(library("httr"))
-suppressPackageStartupMessages(library("rtracklayer"))
-suppressPackageStartupMessages(library("stringr"))
-suppressPackageStartupMessages(library("tools"))
+suppressPackageStartupMessages({
+    library(AnnotationHub)
+    library(argparser)
+    library(ensembldb)
+    library(httr)
+    library(rtracklayer)
+    library(stringr)
+    library(tools)
+})
 
 argp <- arg_parser("Get GDC GENCODE gtf and latest Ensembl annotations")
 argp <- add_argument(

diff --git a/mlcomp.R b/mlcomp.R
@@ -1,10 +1,12 @@
-library(dplyr)
-library(readr)
-library("ggpubr")
-library(VennDiagram)
-library(cowplot)
+suppressPackageStartupMessages({
+  library(dplyr)
+  library(readr)
+  library(ggpubr)
+  library(VennDiagram)
+  library(cowplot)
+  library(RColorBrewer)
+})
 
-library(RColorBrewer)
 myCol <- brewer.pal(3, "Pastel2")
 cbPalette <- c(
   "#999999", "#E69F00", "#56B4E9", "#009E73",

diff --git a/process_knight_data_gdc_meta.R b/process_knight_data_gdc_meta.R
@@ -1,9 +1,11 @@
 options(warn=1)
-suppressPackageStartupMessages(library("argparser"))
-suppressPackageStartupMessages(library("data.table"))
-suppressPackageStartupMessages(library("httr"))
-suppressPackageStartupMessages(library("GenomicDataCommons"))
-suppressPackageStartupMessages(library("stringr"))
+suppressPackageStartupMessages({
+    library(argparser)
+    library(data.table)
+    library(httr)
+    library(GenomicDataCommons)
+    library(stringr)
+})
 
 stopifnot(GenomicDataCommons::status()$status == "OK")
 

diff --git a/process_surv_resp_pdata.R b/process_surv_resp_pdata.R
@@ -1,5 +1,5 @@
 options(warn=1)
-suppressPackageStartupMessages(library("argparser"))
+suppressPackageStartupMessages(library(argparser))
 
 argp <- arg_parser("Process survival and drug response phenotypic data")
 argp <- add_argument(