Merge pull request #112 from samuel-marsh/release/1.1.2

Release/1.1.2

Author: samuel-marsh

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 1.1.1
-Date: 2023-01-13 15:02:59 UTC
-SHA: a78523f9f8648a034a64a2f7455ddb8acfbca410
+Version: 1.1.2
+Date: 2023-07-18 18:13:59 UTC
+SHA: 9546b0eb9894cba46d6c20670e58c60ee3e185cb

DESCRIPTION

@@ -2,8 +2,8 @@ Package: scCustomize
 Type: Package
 Title: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing
 Description: Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'.  'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions.  For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" <doi:10.5281/zenodo.5706430>.
-Version: 1.1.1
-Date: 2023-01-13
+Version: 1.1.2
+Date: 2023-07-18
 Authors@R: c(
     person(given = "Samuel", family = "Marsh", email = "samuel.marsh@childrens.harvard.edu", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3012-6945")),
     person(given = "Ming", family = "Tang", role = c("ctb"), email = "tangming2005@gmail.com"),

NAMESPACE

@@ -33,6 +33,7 @@ export(DimPlot_LIGER)
 export(DimPlot_scCustom)
 export(DiscretePalette_scCustomize)
 export(DotPlot_scCustom)
+export(Extract_Modality)
 export(Extract_Sample_Meta)
 export(Extract_Top_Markers)
 export(FeaturePlot_DualAssay)
@@ -53,6 +54,7 @@ export(Liger_to_Seurat)
 export(Median_Stats)
 export(Merge_Seurat_List)
 export(Merge_Sparse_Data_All)
+export(Merge_Sparse_Multimodal_All)
 export(Meta_Highlight_Plot)
 export(Meta_Numeric)
 export(Meta_Present)
@@ -90,6 +92,7 @@ export(Read_CellBender_h5_Multi_Directory)
 export(Read_CellBender_h5_Multi_File)
 export(Read_GEO_Delim)
 export(Read_Metrics_10X)
+export(Reduction_Loading_Present)
 export(Rename_Clusters)
 export(Replace_Suffix)
 export(Seq_QC_Plot_Alignment_Combined)
@@ -157,6 +160,7 @@ importFrom(SeuratObject,PackageCheck)
 importFrom(circlize,colorRamp2)
 importFrom(cowplot,theme_cowplot)
 importFrom(data.table,fread)
+importFrom(dplyr,across)
 importFrom(dplyr,all_of)
 importFrom(dplyr,any_of)
 importFrom(dplyr,arrange)
@@ -169,14 +173,12 @@ importFrom(dplyr,intersect)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
 importFrom(dplyr,n)
-importFrom(dplyr,one_of)
 importFrom(dplyr,pull)
 importFrom(dplyr,rename)
 importFrom(dplyr,select)
-importFrom(dplyr,select_at)
 importFrom(dplyr,slice)
 importFrom(dplyr,slice_max)
-importFrom(dplyr,summarise_at)
+importFrom(dplyr,summarise)
 importFrom(dplyr,summarize)
 importFrom(forcats,fct_relevel)
 importFrom(ggbeeswarm,geom_quasirandom)
@@ -195,6 +197,7 @@ importFrom(janitor,adorn_totals)
 importFrom(lifecycle,deprecated)
 importFrom(magrittr,"%>%")
 importFrom(methods,as)
+importFrom(methods,hasArg)
 importFrom(methods,new)
 importFrom(methods,slot)
 importFrom(paletteer,paletteer_c)
@@ -203,7 +206,6 @@ importFrom(patchwork,plot_annotation)
 importFrom(patchwork,plot_layout)
 importFrom(patchwork,wrap_plots)
 importFrom(pbapply,pblapply)
-importFrom(pbapply,pbmapply)
 importFrom(pbapply,pboptions)
 importFrom(purrr,discard)
 importFrom(purrr,keep)

NEWS.md

@@ -1,3 +1,33 @@
+# scCustomize 1.1.2 (2023-07-18)  
+## Added  
+- Added `aspect_ratio` parameter to all dimensionality reduction plots to control axes ratio of output plot.  
+- Added `plot_median` and `median_size` parameters to `QC_Plots_*` functions.  
+- Added `split_collect` parameter to `FeaturePlot_scCustom` to collect all guides when using `split.by` for a single feature ([#94](https://github.com/samuel-marsh/scCustomize/issues/94)).  
+- Added new parameters to `Clustered_DotPlot` to allow modification of sizes of column text labels, legend text labels, and legend title labels ([#96](https://github.com/samuel-marsh/scCustomize/issues/96)).  
+- Added new function `Merge_Sparse_Multimodal_All` for merging multi-modal data (1 matrix per modality) ([#104](https://github.com/samuel-marsh/scCustomize/issues/104)).  
+- Added new parameter to `Clustered_DotPlot` named `row_label_fontface` to allow control of fontface used for row labels ([#103](https://github.com/samuel-marsh/scCustomize/issues/103)).  
+- Added helper utility `Reduction_Loading_Present`, in part to fix issue with `FeaturePlot_scCustom` and internal feature checking.  
+- Added ability to turn off feature/ident clustering in `Clustered_DotPlot` using new parameters: `cluster_feature`, `cluster_ident` ([#106](https://github.com/samuel-marsh/scCustomize/issues/106)).  
+- Added `dot_size` parameter to statistics plotting functions `Plot_Cells_per_Sample` and `Plot_Median_*` family.  
+- Added new parameter `no_legend` to `Iterate_Meta_Highlight_Plot` to allow for plotting with a plot title instead of plot legend ([#108](https://github.com/samuel-marsh/scCustomize/issues/108)).  
+  
+  
+## Changed  
+- Moved `QC_Plots_Feature` to use `VlnPlot_scCustom` under the hood like rest of `QC_Plots_*` functions.  
+- Renamed parameter `abort` in `Meta_Present` to `return_none` to align with `Gene_Present` and `Reduction_Loading_Present`.  
+- Replace superseded dplyr syntax/functionality `summarise_at`, `select(.data[[var]])`, and `rename(.data[[var]])` with current dplyr syntax.  
+- Internal rewrite of plotting sections within `Iterate_Cluster_Highlight_Plot` and `Iterate_Meta_Highlight_Plot` to align with recent updates to base `Cluster_Highlight_Plot` and `Meta_Highlight_Plot` functions.  
+   
+
+## Fixes  
+- Fixed `QC_Plots_Feature` to respect parameters when passing to `VlnPlot` ([#91](https://github.com/samuel-marsh/scCustomize/issues/91)).  
+- Fixed `Read_CellBender_h5_*` functions to support CellBender outputs from STARsolo- or Cell Ranger (pre-V3)-processed data ([#99](https://github.com/samuel-marsh/scCustomize/issues/99)).  
+- Fixed `FeaturePlot_scCustom` to allow for plotting of dimensionality reduction loadings ([#97](https://github.com/samuel-marsh/scCustomize/issues/97)).  
+- Fixed `Read10X_Multi_Directory` and `Read10X_h5_Multi_Directory` to support files processed with Cell Ranger `multi` pipeline.  
+- Fixed bug in `Merge_Seurat_List` that prevented `add.cell.id` from adding correct cell name prefixes ([#113](https://github.com/samuel-marsh/scCustomize/issues/113)).  
+   
+
+
 # scCustomize 1.1.1 (2023-01-13)  
 ## Added  
 - Added `label_color_num` parameter to `PalettePlot` allow control of color labeling.  
@@ -21,6 +51,7 @@
 - Updated out-dated documentation for number of package functions.  
 - Typo/styling fixes.  
 
+ 
 # scCustomize 1.1.0 (2022-12-22)  
 ## Added  
 - Added `merge` parameter to `Read10X_GEO`, `Read10X_h5_GEO`, `Read_GEO_Delim` and `Read_CellBender_h5_Multi_File`.  

R/Color_Palettes.R

@@ -182,14 +182,14 @@ Single_Color_Palette <- function(pal_color,
       "#000000"
     )
   )
-  if (!pal_color %in% names(brewer_single_modified)) {
+  if (!pal_color %in% names(x = brewer_single_modified)) {
     cli_abort(message = c("Paleete name not found.",
                           "i" = "Palette name not found.  Please select one of following palette options: {.field 'reds', 'blues', 'greens', 'purples', or 'grays'}")
     )
   }
   set.seed(seed = seed_use)
   pal_use <- brewer_single_modified[[pal_color]]
-  output_pal <- sample(pal_use, size = num_colors)
+  output_pal <- sample(x = pal_use, size = num_colors)
   return(output_pal)
 }
 
@@ -216,7 +216,7 @@ NavyAndOrange <- function(
 ) {
   navy_orange <- c("navy", "orange")
   if (flip_order) {
-    navy_orange <- rev(navy_orange)
+    navy_orange <- rev(x = navy_orange)
   }
   return(navy_orange)
 }
@@ -356,8 +356,8 @@ ColorBlind_Pal <- function(
 varibow_scCustom <- function(
   n_colors
 ) {
-  sats <- rep_len(c(0.55,0.7,0.85,1),length.out = n_colors)
-  vals <- rep_len(c(1,0.8,0.6),length.out = n_colors)
+  sats <- rep_len(x = c(0.55,0.7,0.85,1), length.out = n_colors)
+  vals <- rep_len(x = c(1,0.8,0.6), length.out = n_colors)
   rainbow(n_colors, s = sats, v = vals)
 }
 
@@ -469,7 +469,7 @@ DiscretePalette_scCustomize <- function(
   }
   if (shuffle_pal) {
     set.seed(seed = seed)
-    palette_out <- sample(palette_out[1:num_colors])
+    palette_out <- sample(x = palette_out[1:num_colors])
   } else {
     palette_out <- palette_out[1:num_colors]
   }

R/Internal_Utilities.R

@@ -225,8 +225,8 @@ glue_collapse_scCustom <- function(
 
 #' Perform Feature and Meta Checks before plotting
 #'
-#' Wraps the `Gene_Present`, `Meta_Present`, and `Case_Check` into single function to perform feature
-#' checks before plotting.
+#' Wraps the `Gene_Present`, `Meta_Present`, `Reduction_Loading_Present`, and `Case_Check` into
+#' single function to perform feature checks before plotting.
 #'
 #' @param object Seurat object
 #' @param features vector of features and/or meta data variables to plot.
@@ -245,11 +245,13 @@ Feature_PreCheck <- function(
   # Check features and meta to determine which features present
   features_list <- Gene_Present(data = object, gene_list = features, omit_warn = FALSE, print_msg = FALSE, case_check_msg = FALSE, return_none = TRUE)
 
-  meta_list <- Meta_Present(seurat_object = object, meta_col_names = features_list[[2]], omit_warn = FALSE, print_msg = FALSE, abort = FALSE)
+  meta_list <- Meta_Present(seurat_object = object, meta_col_names = features_list[[2]], omit_warn = FALSE, print_msg = FALSE, return_none = TRUE)
 
-  all_not_found_features <- meta_list[[2]]
+  reduction_list <- Reduction_Loading_Present(seurat_object = object, reduction_names = meta_list[[2]], omit_warn = FALSE, print_msg = FALSE, return_none = TRUE)
 
-  all_found_features <- c(features_list[[1]], meta_list[[1]])
+  all_not_found_features <- reduction_list[[2]]
+
+  all_found_features <- c(features_list[[1]], meta_list[[1]], reduction_list[[1]])
 
   # Stop if no features found
   if (length(x = all_found_features) < 1) {

R/LIGER_Plotting.R

@@ -18,6 +18,8 @@
 #' @param shuffle_seed Sets the seed if randomly shuffling the order of points.
 #' @param reduction_label What to label the x and y axes of resulting plots.  LIGER does not store name of
 #' technique and therefore needs to be set manually.  Default is "UMAP".
+#' @param aspect_ratio Control the aspect ratio (y:x axes ratio length).  Must be numeric value;
+#' Default is NULL.
 #' @param label logical.  Whether or not to label the clusters.  ONLY applies to plotting by cluster.  Default is TRUE.
 #' @param label_size size of cluster labels.
 #' @param label_repel logical.  Whether to repel cluster labels from each other if plotting by
@@ -61,6 +63,7 @@ DimPlot_LIGER <- function(
   shuffle = TRUE,
   shuffle_seed = 1,
   reduction_label = "UMAP",
+  aspect_ratio = NULL,
   label = TRUE,
   label_size = NA,
   label_repel = FALSE,
@@ -170,6 +173,15 @@ DimPlot_LIGER <- function(
                              shuffle_seed = shuffle_seed)
 
     p3 <- wrap_plots(p1 + p2)
+
+    # Aspect ratio changes
+    if (!is.null(x = aspect_ratio)) {
+      if (!is.numeric(x = aspect_ratio)) {
+        cli_abort(message = "{.code aspect_ratio} must be a {.field numeric} value.")
+      }
+      p3 <- p3 & theme(aspect.ratio = aspect_ratio)
+    }
+
     return(p3)
   }
 
@@ -192,6 +204,14 @@ DimPlot_LIGER <- function(
                                 label_color = label_color,
                                 label = label,
                                 color_seed = color_seed)
+    # Aspect ratio changes
+    if (!is.null(x = aspect_ratio)) {
+      if (!is.numeric(x = aspect_ratio)) {
+        cli_abort(message = "{.code aspect_ratio} must be a {.field numeric} value.")
+      }
+      p1 <- p1 & theme(aspect.ratio = aspect_ratio)
+    }
+
     return(p1)
   }
 
@@ -210,6 +230,14 @@ DimPlot_LIGER <- function(
                              split_by = split_by,
                              shuffle_seed = shuffle_seed,
                              color_seed = color_seed)
+    # Aspect ratio changes
+    if (!is.null(x = aspect_ratio)) {
+      if (!is.numeric(x = aspect_ratio)) {
+        cli_abort(message = "{.code aspect_ratio} must be a {.field numeric} value.")
+      }
+      p2 <- p2 & theme(aspect.ratio = aspect_ratio)
+    }
+
     return(p2)
   }
 }
@@ -330,7 +358,7 @@ plotFactors_scCustom <- function(
                             "i" = "The number of datasets provided to {.code reorder_datasets} ({.field {length(x = reorder_datasets)}}) does not match number of datasets in LIGER object ({.field {length(x = levels(x = levels(liger_object@cell.data$dataset)))}}).")
       )
     } else {
-      if (!all(levels(liger_object@cell.data$dataset) %in% reorder_datasets)) {
+      if (!all(levels(x = liger_object@cell.data$dataset) %in% reorder_datasets)) {
         cli_abort(message = c("Error reordering datasets (name mismatch).",
                               "*" = "Dataset names provided to {.code reorder_datasets} do not match names of datasets in LIGER object.",
                               "i" = "Please check spelling.")
@@ -379,16 +407,16 @@ plotFactors_scCustom <- function(
 
   # Get Data and Plot Factors
   cli_inform(message = "{.field Generating plots}")
-  k <- ncol(liger_object@H.norm)
+  k <- ncol(x = liger_object@H.norm)
   pb <- txtProgressBar(min = 0, max = k, style = 3)
-  W <- t(liger_object@W)
-  rownames(W) <- colnames(liger_object@scale.data[[1]])
+  W <- t(x = liger_object@W)
+  rownames(x = W) <- colnames(x = liger_object@scale.data[[1]])
   Hs_norm <- liger_object@H.norm
   H_raw = do.call(rbind, liger_object@H)
   plot_list = list()
   tsne_list = list()
   for (i in 1:k) {
-    top_genes.W <- rownames(W)[order(W[, i], decreasing = T)[1:num_genes]]
+    top_genes.W <- rownames(x = W)[order(W[, i], decreasing = T)[1:num_genes]]
     top_genes.W.string <- paste0(top_genes.W, collapse = ", ")
     factor_textstring <- paste0("Factor", i)
     plot_title1 <- paste(factor_textstring, "\n", top_genes.W.string, "\n")
@@ -461,7 +489,7 @@ plotFactors_scCustom <- function(
     if (plot_dimreduc) {
       tsne_df <- data.frame(Hs_norm[, i], liger_object@tsne.coords)
       factorlab <- paste0("Factor", i)
-      colnames(tsne_df) <- c(factorlab, x_axis_label, y_axis_label)
+      colnames(x = tsne_df) <- c(factorlab, x_axis_label, y_axis_label)
 
       if (order) {
         tsne_df <- tsne_df[order(tsne_df[,1], decreasing = FALSE),]