compatibility with R 4.1.0, better docs and added imports

Author: darlanminussi

DESCRIPTION

@@ -63,7 +63,11 @@ Imports:
     gtools,
     forcats,
     circlize,
-    BiocParallel
+    BiocParallel,
+    fpc,
+    ggnewscale,
+    miniUI,
+    pals
 RoxygenNote: 7.1.1
 VignetteBuilder: knitr
 Depends: 

NAMESPACE

@@ -130,6 +130,7 @@ importFrom(shiny,checkboxGroupInput)
 importFrom(shiny,fillCol)
 importFrom(shiny,plotOutput)
 importFrom(shiny,stopApp)
+importFrom(stringr,fixed)
 importFrom(stringr,str_detect)
 importFrom(stringr,str_extract)
 importFrom(stringr,str_remove)

R/plotUmap.R

@@ -80,8 +80,9 @@ plotUmap <- function(scCNA,
       ),
       size = 1.8,
       shape = 21) +
-    scale_fill_manual(values = c(subclones_pal()),
-                       name = "subclones") +
+    scale_fill_manual(values = subclones_pal(),
+                       name = "subclones",
+                      limits = force) +
     theme_classic() +
       my_theme
 
@@ -110,8 +111,9 @@ plotUmap <- function(scCNA,
       ),
       size = 1.8,
       shape = 21) +
-      scale_fill_manual(values = c(subclones_pal()),
-                        name = "subclones") + # palettes are in sysdata.rda
+      scale_fill_manual(values = subclones_pal(),
+                        name = "subclones",
+                        limits = force) +
       theme_classic() +
       my_theme
 

R/runCountReads.R

@@ -17,7 +17,7 @@
 #' @return Genomic ranges can be accessed with \code{SummarizedExperiment::rowRanges()}
 #'
 #' @importFrom Rsubread featureCounts
-#' @importFrom stringr str_replace str_remove str_detect
+#' @importFrom stringr str_replace str_remove str_detect fixed
 #' @importFrom dplyr rename mutate relocate
 #' @importFrom GenomicRanges makeGRangesFromDataFrame
 #' @importFrom S4Vectors DataFrame metadata
@@ -114,7 +114,13 @@ runCountReads <- function(dir,
                                '[[',
                                1)
 
-  names(varbin_counts_list) <- files_names
+  varbin_counts_list <- lapply(varbin_counts_list,
+                               as.vector)
+
+  names(varbin_counts_list) <- stringr::str_remove(files_names,
+                                                   stringr::fixed(".bam",
+                                                                  ignore_case = TRUE))
+
 
   #LOWESS GC normalization
 
@@ -166,7 +172,9 @@ runCountReads <- function(dir,
                               '[[',
                               4)
 
-  names(varbin_reads_list) <- files_names
+  names(varbin_reads_list) <- stringr::str_remove(files_names,
+                                                  stringr::fixed(".bam",
+                                                                 ignore_case = TRUE))
 
   # saving info and removing columns from list elements
   metadata_info_names <- varbin_reads_list[[1]][c(1, 2, 8, 9, 12, 14), 1]

R/runSegmentation.R

@@ -14,6 +14,7 @@
 #' @importFrom dplyr mutate bind_cols
 #' @importFrom stringr str_detect str_remove str_replace
 #' @importFrom S4Vectors metadata
+#' @importFrom SummarizedExperiment assay
 #' @importFrom BiocParallel bplapply bpparam
 #' @importMethodsFrom SummarizedExperiment assay
 #' @export
@@ -88,10 +89,12 @@ runSegmentation <- function(scCNA,
 
   }
 
+
+
   if (method == "CBS") {
 
     if (S4Vectors::metadata(scCNA)$vst == 'ft') {
-      counts_df <- assay(scCNA, 'ft')
+      counts_df <- SummarizedExperiment::assay(scCNA, 'ft')
 
       CBS_seg <- BiocParallel::bplapply(counts_df, FUN = function(x) {
         CNA_object <-
@@ -129,7 +132,7 @@ runSegmentation <- function(scCNA,
               noBreaks. = TRUE)
       # segmentation with undo.splits = "prune"
 
-      counts_df <- assay(scCNA, 'log')
+      counts_df <- SummarizedExperiment::assay(scCNA, 'log')
 
       CBS_seg <-
         BiocParallel::bplapply(as.data.frame(counts_df), function(x) {

R/runVarbin.R

@@ -82,6 +82,8 @@ runVarbin <- function(dir,
                       name = 'segment_ratios',
                       BPPARAM = bpparam()) {
 
+  genome <- match.arg(genome)
+  vst <- match.arg(vst)
 
   copykit_object <- runCountReads(dir,
                                   bin_size = bin_size,

R/runVst.R

@@ -28,6 +28,8 @@
 runVst <- function(scCNA,
                    transformation = c('ft','log')) {
 
+  transformation <- match.arg(transformation)
+
   varbin_counts_df <- copykit::bin_counts(scCNA)
 
   if (transformation == 'ft') {