fix: resolve gDRstyle linting violations

.gitignore

@@ -46,3 +46,4 @@ vignettes/*.pdf
 # support for build via github.com with access_token defined
 .github_access_token.txt
 docs
+.serena/

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: gDRutils
 Type: Package
 Title: A package with helper functions for processing drug response data
-Version: 1.11.2
+Version: 1.11.3
 Date: 2026-05-05
 Authors@R: c(person("Bartosz", "Czech", role=c("aut"),
                    comment = c(ORCID = "0000-0002-9908-3007")),

NEWS.md

@@ -1,3 +1,6 @@
+## gDRutils 1.11.3 - 2026-05-18
+* apply updated gDRstyle rules
+
 ## gDRutils 1.11.2 - 2026-05-05
 * update author email address
 
@@ -727,4 +730,4 @@
 * import pipes from magrittr
 
 ## gDRutils 0.0.0.4 - 2020-06-10
-* including the masked field to be able to remove the masked data from averages
+* including the masked field to be able to remove the masked data from averages

R/assay_names.R

@@ -22,10 +22,10 @@ ASSAY_INFO_TBL <- data.table::data.table(
 #'    will return single string instead of named vector with single element
 #'    useful when function is expected to return single element/assay only
 #' @keywords assay_names
-#'    
+#'
 #' @return charvec
-#' 
-#' @examples 
+#'
+#' @examples
 #' get_env_assay_names()
 #'
 #' @author Arkadiusz Gładki \email{arkadiusz.gladki@@contractors.roche.com}
@@ -66,7 +66,7 @@ get_env_assay_names <-
       df <- df[df[[eval(filter)]] %in% v_filters[[filter]], ]
     }
 
-    if ((nrow(df)) == 0)  {
+    if ((NROW(df)) == 0)  {
       v_filters_str <-
         paste(names(v_filters),
               v_filters,
@@ -93,9 +93,9 @@ get_env_assay_names <-
 #'
 #' @return  charvec
 #'
-#' @examples 
+#' @examples
 #' get_assay_names()
-#' 
+#'
 #' @export
 get_assay_names <- function(se = NULL, ...) {
   if (!is.null(se) &&
@@ -116,9 +116,9 @@ get_assay_names <- function(se = NULL, ...) {
 #' @keywords assay_names
 #' @return charvec of combo assay names.
 #' @export
-#' @examples 
+#' @examples
 #' get_combo_assay_names()
-#' 
+#'
 #' @author Arkadiusz Gładki \email{arkadiusz.gladki@@contractors.roche.com}
 #'
 get_combo_assay_names <- function(se = NULL, ...) {
@@ -134,7 +134,7 @@ get_combo_assay_names <- function(se = NULL, ...) {
 #' @return  charvec
 #' @export
 #'
-#' @examples 
+#' @examples
 #' get_combo_base_assay_names()
 #' @author Arkadiusz Gładki \email{arkadiusz.gladki@@contractors.roche.com}
 #'
@@ -151,10 +151,10 @@ get_combo_base_assay_names <- function(se = NULL, ...) {
 #' @return  charvec
 #'
 #' @export
-#' 
-#' @examples 
+#'
+#' @examples
 #' get_combo_score_assay_names()
-#' 
+#'
 #' @author Arkadiusz Gładki \email{arkadiusz.gladki@@contractors.roche.com}
 #'
 get_combo_score_assay_names <- function(se = NULL, ...) {

R/combo.R

@@ -3,14 +3,14 @@
 #' @param se \code{SummarizedExperiment} object with dose-response data
 #' @param c_assays charvec of combo assays to be used
 #' @param normalization_type charvec of normalization_types expected in the data
-#' @param prettify boolean flag indicating whether or not to prettify the colnames of the returned data 
+#' @param prettify boolean flag indicating whether or not to prettify the colnames of the returned data
 #' @keywords combination_data
-#' 
+#'
 #' @author Arkadiusz Gładki \email{arkadiusz.gladki@@contractors.roche.com}
 #'
 #' @return list of data.table(s) with combo data
 #'
-#' @examples 
+#' @examples
 #' mae <- get_synthetic_data("finalMAE_combo_matrix_small.qs2")
 #' convert_combo_data_to_dt(mae[[1]])
 #'
@@ -38,7 +38,7 @@ convert_combo_data_to_dt <-
         }
         dt
       })
-    
+
     # TODO: discuss what should be returned: assay_name or maybe assay_type?
     names(my_l) <- as.character(c_assays)
     my_l
@@ -60,10 +60,10 @@ DATA_COMBO_INFO_TBL <- data.table::data.table(
 #' @return  charvec
 #'
 #' @export
-#' 
-#' @examples 
+#'
+#' @examples
 #' get_combo_score_assay_names()
-#' 
+#'
 get_combo_score_field_names <- function() {
   dt <- DATA_COMBO_INFO_TBL[type == "scores", c("name", "pname"), with = FALSE]
   stats::setNames(dt$pname, dt$name)
@@ -75,10 +75,10 @@ get_combo_score_field_names <- function() {
 #' @return charvec
 #'
 #' @export
-#' 
-#' @examples 
+#'
+#' @examples
 #' get_combo_excess_field_names()
-#' 
+#'
 get_combo_excess_field_names <- function() {
   dt <- DATA_COMBO_INFO_TBL[type == "excess", c("name", "pname"), with = FALSE]
   stats::setNames(dt$pname, dt$name)
@@ -93,10 +93,10 @@ get_combo_excess_field_names <- function() {
 #' @return charvec
 #'
 #' @export
-#' 
-#' @examples 
+#'
+#' @examples
 #' convert_combo_field_to_assay("hsa_score")
-#' 
+#'
 convert_combo_field_to_assay <- function(field) {
   checkmate::assert_string(field)
   DATA_COMBO_INFO_TBL[name == field, ][["type"]]
@@ -111,26 +111,26 @@ convert_combo_field_to_assay <- function(field) {
 #' @details
 #' \code{drug_1} is diluted along the rows as the y-axis and
 #' \code{drug_2} is diluted along the columns and will be the x-axis.
-#' 
+#'
 #' @keywords combination_data
 #' @return list with axis grid positions
-#' 
+#'
 #' @examples
 #' cl_name <- "cellline_BC"
 #' drug1_name <- "drug_001"
 #' drug2_name <- "drug_026"
-#' 
+#'
 #' se <- get_synthetic_data("combo_matrix_small")[["combination"]]
 #' dt_average <- convert_se_assay_to_dt(se, "Averaged")[normalization_type == "GR"]
-#' 
+#'
 #' ls_axes <- define_matrix_grid_positions(
 #'    dt_average[["Concentration"]], dt_average[["Concentration_2"]])
-#' 
+#'
 #' @export
 define_matrix_grid_positions <- function(conc1, conc2) {
   checkmate::assert_numeric(conc1)
   checkmate::assert_numeric(conc2)
-  
+
   .generate_gap_for_single_agent <- function(x) {
     if (NROW(x) == 1) {
       x
@@ -139,8 +139,8 @@ define_matrix_grid_positions <- function(conc1, conc2) {
     } else {
       x[2] - 0.5 # diff(log10(c(0, 10^(seq(-3, 1, 0.5))))) # nolint
     }
-  } 
-  
+  }
+
   conc_1 <- sort(unique(round_concentration(conc1)))
   pos_y <- log10conc_1 <- log10(conc_1)
   pos_y[1] <- .generate_gap_for_single_agent(log10conc_1)
@@ -149,7 +149,7 @@ define_matrix_grid_positions <- function(conc1, conc2) {
                                    pos_y = pos_y,
                                    marks_y = sprintf("%.2g", conc_1)
   )
-  
+
   conc_2 <- sort(unique(round_concentration(conc2)))
   pos_x <- log10conc_2 <- log10(conc_2)
   pos_x[1] <- .generate_gap_for_single_agent(log10conc_2)
@@ -158,16 +158,16 @@ define_matrix_grid_positions <- function(conc1, conc2) {
                                    pos_x = pos_x,
                                    marks_x = sprintf("%.2g", conc_2)
   )
-  
+
   list(axis_1 = axis_1, axis_2 = axis_2)
 }
 
 #' Round concentration to ndigit significant digits
 #'
 #' @param x value to be rounded.
 #' @param ndigit number of significant digits (default = 4).
-#' 
-#' @examples 
+#'
+#' @examples
 #' round_concentration(x = c(0.00175,0.00324,0.0091), ndigit = 1)
 #'
 #' @return rounded x
@@ -176,6 +176,6 @@ define_matrix_grid_positions <- function(conc1, conc2) {
 round_concentration <- function(x, ndigit = 3) {
   checkmate::assert_numeric(x)
   checkmate::assert_integerish(ndigit)
-  
+
   round(10 ^ (round(log10(x), ndigit)), ndigit - 1 - floor(log10(x)))
 }

R/concatentate_SEs.R

@@ -31,13 +31,13 @@ has_nested_field <- function(asy, nested_field) {
 #'
 #' @seealso promote_fields
 #' @details Revert this operation using \code{promote_fields}.
-#' 
-#' @examples 
+#'
+#' @examples
 #' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' se <- mae[[1]]
 #' se <- promote_fields(se, "ReadoutValue", 2)
 #' demote_fields(se, "ReadoutValue")
-#' 
+#'
 #' @export
 demote_fields <- function(se, fields) {
   checkmate::assertClass(se, "SummarizedExperiment")
@@ -48,7 +48,7 @@ demote_fields <- function(se, fields) {
 
   if (any(are_nested_fields <- !fields %in% c(rowmd, colmd))) {
     stop(sprintf("field(s) '%s' are already demoted fields, perhapy you intended to call 'promote_fields'?",
-                 paste0(fields[are_nested_fields], collapse = ", ")))
+                 toString(fields[are_nested_fields])))
   }
 
   rowmd <- setdiff(rowmd, fields)
@@ -94,26 +94,26 @@ demote_fields <- function(se, fields) {
 #' @return A \code{SummarizedExperiment} object with new dimensions resulting from promoting given \code{fields}.
 #' @details Revert this operation using \code{demote_fields}.
 #' @seealso demote_fields
-#' 
-#' @examples 
+#'
+#' @examples
 #' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' se <- mae[[1]]
 #' se <- promote_fields(se, "ReadoutValue", 2)
-#' 
+#'
 #' @export
 promote_fields <- function(se, fields, MARGIN = c(1, 2)) {
   checkmate::assertClass(se, "SummarizedExperiment")
   checkmate::assertCharacter(fields)
   if (length(MARGIN) != 1L || !MARGIN %in% c(1, 2)) {
     stop("invalid 'MARGIN' argument, must be either '1' or '2'")
   }
-  rowmd <- colnames(rowData(se)) 
+  rowmd <- colnames(rowData(se))
   colmd <- colnames(colData(se))
   rowmd <- colnames(rowData(se))
   colmd <- colnames(colData(se))
   if (any(rfields <- fields %in% rowmd) || any(cfields <- fields %in% colmd)) {
     stop(sprintf("fields '%s' are already promoted fields",
-                 paste0(fields[rfields || cfields], collapse = ", ")))
+                 toString(fields[rfields || cfields])))
   }
   if (MARGIN == 1) {
     rowmd <- c(rowmd, fields)
@@ -139,7 +139,7 @@ promote_fields <- function(se, fields, MARGIN = c(1, 2)) {
   }
   if (length(final_assays) == 0L) {
     stop(sprintf("unable to find nested fields: '%s' in any assays, perhaps you intended to call 'demote_fields'?",
-                 paste0(fields, collapse = ", ")))
+                 toString(fields)))
   }
   .validate_final_assays(final_assays)
   assay_list <- lapply(final_assays, function(x) {
@@ -184,7 +184,7 @@ promote_fields <- function(se, fields, MARGIN = c(1, 2)) {
   missing <- setdiff(colnames(df), c(row_fields, column_fields, nested_fields))
   if (length(missing) != 0L) {
     stop(sprintf("found columns in 'df' not specified as row, column, or nested fields",
-                 paste0(missing, collapse = ", ")))
+                 toString(missing)))
   }
   if (any(is_duplicated <- duplicated(c(row_fields, column_fields, nested_fields)))) {
     stop(sprintf("fields: '%s' are duplicated across arguments 'row_fields', 'column_fields', 'nested_fields'",
@@ -216,13 +216,13 @@ promote_fields <- function(se, fields, MARGIN = c(1, 2)) {
 #' @keywords SE_operators
 #'
 #' @return A \code{BumpyMatrix} object aggregated by \code{FUN}.
-#' 
-#' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs2") 
+#'
+#' @examples
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' se <- mae[[1]]
 #' assay <- SummarizedExperiment::assay(se)
 #' aggregate_assay(assay, FUN = mean, by = c("Barcode"))
-#' 
+#'
 #' @export
 aggregate_assay <- function(asy, by, FUN) {
   checkmate::assert_class(asy, "BumpyMatrix")
@@ -238,7 +238,7 @@ aggregate_assay <- function(asy, by, FUN) {
                                         row.field = row.field,
                                         column.field = column.field)
   if (!all(present <- by %in% setdiff(colnames(df), c(row.field, column.field)))) {
-    stop(sprintf("specified 'by' columns: '%s' are not present in 'asy'", paste0(by[!present], collapse = ", ")))
+    stop(sprintf("specified 'by' columns: '%s' are not present in 'asy'", toString(by[!present])))
   }
 
   by <- c(row.field, column.field, by)