style: conform to BiocChceck recommedned coding style

CogDisResLab · Sep 7, 2023 · 7883976 · 7883976
1 parent 82a0b2a
commit 7883976
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Showing 5 changed files with 27 additions and 31 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -90,7 +90,7 @@ repos:
     -   id: style_files
         name: Apply bioconductor style
         entry: >
-            Rscript -e "styler::style_pkg(transformers = biocthis::bioc_style())"
+            Rscript -e "styler::style_pkg(transformers = styler::tidyverse_style(indent_by = 4))"
         language: system
     -   id: lint_files
         name: Apply lintr

diff --git a/R/consensus_concordants.R b/R/consensus_concordants.R
@@ -44,11 +44,10 @@ target_rename <- function(input_names) {
 #'
 #' @examples
 #' TRUE
-consensus_concordants <- function(
-        ...,
-        paired = FALSE,
-        cutoff = 0.321,
-        cell_line = NULL) {
+consensus_concordants <- function(...,
+                                  paired = FALSE,
+                                  cutoff = 0.321,
+                                  cell_line = NULL) {
     if (paired && length(list(...)) != 2L) {
         stop("Paired analysis requires two data frames")
     } else if (!paired && length(list(...)) != 1L) {

diff --git a/R/investigate_signature.R b/R/investigate_signature.R
@@ -29,21 +29,20 @@
 #'
 #' @examples
 #' TRUE
-investigate_signature <- function(
-        expr,
-        output_lib,
-        filter_threshold = NULL,
-        filter_prop = NULL,
-        similarity_threshold = 0.2,
-        paired = TRUE,
-        output_cell_lines = NULL,
-        gene_column = "Symbol",
-        logfc_column = "logFC",
-        pval_column = "PValue",
-        source_name = "Input",
-        source_cell_line = "NA",
-        source_time = "NA",
-        source_concentration = "NA") {
+investigate_signature <- function(expr,
+                                  output_lib,
+                                  filter_threshold = NULL,
+                                  filter_prop = NULL,
+                                  similarity_threshold = 0.2,
+                                  paired = TRUE,
+                                  output_cell_lines = NULL,
+                                  gene_column = "Symbol",
+                                  logfc_column = "logFC",
+                                  pval_column = "PValue",
+                                  source_name = "Input",
+                                  source_cell_line = "NA",
+                                  source_time = "NA",
+                                  source_concentration = "NA") {
     libs <- c("OE", "KD", "CP")
 
     if (!output_lib %in% libs) {

diff --git a/R/investigate_target.R b/R/investigate_target.R
@@ -26,11 +26,10 @@
 #'
 #' @examples
 #' TRUE
-investigate_target <- function(
-        target, input_lib, output_lib,
-        filter_threshold = 0.85, similarity_threshold = 0.321,
-        paired = TRUE, input_cell_lines = NULL,
-        output_cell_lines = NULL, discordant = FALSE) {
+investigate_target <- function(target, input_lib, output_lib,
+                               filter_threshold = 0.85, similarity_threshold = 0.321,
+                               paired = TRUE, input_cell_lines = NULL,
+                               output_cell_lines = NULL, discordant = FALSE) {
     libs <- c("OE", "KD", "CP")
 
     if (!input_lib %in% libs || !output_lib %in% libs) {

diff --git a/R/prepare_signature.R b/R/prepare_signature.R
@@ -20,11 +20,10 @@
 #'
 #' @examples
 #' TRUE
-prepare_signature <- function(
-        dge,
-        gene_column = "Symbol",
-        logfc_column = "logFC",
-        pval_column = "PValue") {
+prepare_signature <- function(dge,
+                              gene_column = "Symbol",
+                              logfc_column = "logFC",
+                              pval_column = "PValue") {
     if (!gene_column %in% names(dge)) {
         stop("gene_column should be present in the dataframe")
     }