removing stringr from dependencies

Author: darlanminussi

DESCRIPTION

@@ -2,7 +2,7 @@ Package: copykit
 Title: CopyKit
 URL: https://github.com/navinlabcode/copykit
 BugReports: https://github.com/navinlabcode/copykit/issues
-Version: 0.0.0.9042
+Version: 0.0.0.9043
 Authors@R: c(
     person(given = "Darlan",
            family = "Conterno Minussi",
@@ -36,7 +36,8 @@ Suggests:
     spelling,
     knitr,
     scquantum,
-    rmarkdown
+    rmarkdown,
+    stringr
 Language: en-US
 biocViews: Software, SingleCell, DNASeq, Sequencing, 
            Visualization, Normalization, Clustering,
@@ -60,7 +61,6 @@ Imports:
     igraph (>= 1.2.8),
     BiocGenerics,
     grid,
-    stringr,
     ggbeeswarm,
     dbscan,
     mixtools,

NAMESPACE

@@ -180,11 +180,6 @@ importFrom(stats,rpois)
 importFrom(stats,runif)
 importFrom(stats,sd)
 importFrom(stats,wilcox.test)
-importFrom(stringr,fixed)
-importFrom(stringr,str_detect)
-importFrom(stringr,str_extract)
-importFrom(stringr,str_remove)
-importFrom(stringr,str_replace)
 importFrom(tidyr,complete)
 importFrom(tidyr,gather)
 importFrom(tidyr,pivot_wider)
@@ -194,3 +189,4 @@ importFrom(withr,with_seed)
 importMethodsFrom(SingleCellExperiment,show)
 importMethodsFrom(SummarizedExperiment,assay)
 importMethodsFrom(SummarizedExperiment,colData)
+importMethodsFrom(SummarizedExperiment,rowRanges)

R/plotHeatmap.R

@@ -6,7 +6,7 @@
 #' @author Darlan Conterno Minussi
 #'
 #' @param scCNA scCNA object.
-#' @param assay String with the name of the assay to pull data from to plot heatmap.
+#' @param assay String with the assay to pull data from to plot heatmap.
 #' @param order_cells A string with the desired method to order the cells within
 #' @param label A vector with the string names of the columns from
 #' \code{\link[SummarizedExperiment]{colData}} for heatmap annotation.
@@ -19,7 +19,7 @@
 #' \code{\link[SummarizedExperiment]{colData}} to split the heatmap.
 #' @param rounding_error A boolean indicating if the rounding error matrix
 #' should be plotted.
-#' @param genes A character vector with the HUGO symbol for genes to be annotated
+#' @param genes A character vector with the HUGO symbol for genes to annotate
 #' on the heatmap.
 #' @param col A colorRamp2 vector that controls the color scale of the heatmap.
 #' See \code{\link[ComplexHeatmap]{Heatmap}} or ComplexHeatmap online docs for
@@ -44,7 +44,7 @@
 #'    \code{\link{plotHeatmap}} checks for the existence of a consensus matrix.
 #'    From the consensus matrix, a minimum evolution tree is built and cells are
 #'     ordered following the order of their respective groups from the tree.
-#'     If order_cells is set to 'hclust' cells are ordered according to hierarchical
+#'     If order_cells is 'hclust' cells are ordered according to hierarchical
 #'      clustering. 'hclust' calculation can be sped up by changing the parameter
 #'      'n_threads' if you have more threads available to use. If order_cells
 #'      is set to 'phylogeny' \code{\link{plotHeatmap}} will use the tree stored
@@ -648,17 +648,18 @@ plotHeatmap <- function(scCNA,
                 c("superclones", "subclones", "outlier", "is_aneuploid")
 
             for (i in 1:length(label)) {
-                if (any(str_detect(
-                    label[i],
-                    default_labels
+                if (any(grepl(
+                    paste(default_labels, collapse = "|"),
+                    label[i]
                 ))) {
                     # if label is one of the four above,
                     # uses the default specified colors above
                     label_colors[i] <-
-                        label_colors[default_labels[stringr::str_detect(
-                            label[i],
-                            default_labels
-                        )]]
+                        label_colors[default_labels[
+                            vapply(default_labels,
+                                   function(x) grepl(x, label[i]),
+                                   logical(1))
+                        ]]
                     names(label_colors)[i] <- label[i]
                 } else if (is.numeric(dplyr::pull(metadata_anno_df, label[i]))) {
                     # if current i metadata element is a numeric vector

R/plotPhylo.R

@@ -52,7 +52,8 @@ plotPhylo <- function(scCNA,
             consensusPhylo(scCNA),
             error = function(e) {
                 stop(
-                    "No consensus phylogeny detected in scCNA object. Please run runConsensusPhylo() first."
+                    "No consensus phylogeny detected in scCNA object.
+                    Please run runConsensusPhylo() first."
                 )
             }
         )
@@ -174,10 +175,12 @@ plotPhylo <- function(scCNA,
             )
 
             if (any(grepl(
-                c("superclones", "subclones", "outlier", "is_aneuploid"),
+                paste(c("superclones", "subclones", "outlier", "is_aneuploid"),
+                      collapse = "|"),
                 label
             ))) {
-                # if label is one of the four above, uses the default specified colors above
+                # if label is one of the four above, uses the default specified
+                # colors above
                 label_colors <- label_colors[[label]]
             } else {
                 elements <- metadata_anno_df %>%

man/plotHeatmap.Rd

@@ -5,8 +5,6 @@ copykit_obj <- copykit_obj[, sample(70)]
 copykit_obj <- findClusters(copykit_obj)
 copykit_obj <- calcConsensus(copykit_obj)
 copykit_obj <- runConsensusPhylo(copykit_obj)
-colData(copykit_obj)$section <- stringr::str_extract(colData(copykit_obj)$sample,
-                                                     "(L[0-9]+L[0-9]+|L[0-9]+)")
 
 #tests
 
@@ -17,13 +15,8 @@ test_that("Testing plotting heatmap: ", {
   expect_s4_class(ht <-
                     plotHeatmap(copykit_obj, label = "subclones"),
                   "Heatmap")
-  expect_s4_class(ht <- plotHeatmap(copykit_obj,
-                                    label = c("section", "subclones")),
-                  "Heatmap")
+
   expect_s4_class(ht <- plotHeatmap(copykit_obj, genes = c("MYC",
                                                            "TP53")),
                   "Heatmap")
-  expect_s4_class(ht <- plotHeatmap(copykit_obj, group = "section"),
-                  "Heatmap")
-
 })