From 852cd93b87a6d6abbda6639904edcd9eac43f29f Mon Sep 17 00:00:00 2001
From: samuel-marsh <samuel.marsh@childrens.harvard.edu>
Date: Fri, 6 Dec 2024 09:14:40 -0500
Subject: [PATCH 01/26] bump dev branch

---
 DESCRIPTION |  4 ++--
 NEWS.md     | 13 +++++++++++++
 2 files changed, 15 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a17e09d54..3f8cf27c6 100644
--- a/DESCRIPTION
+++ b/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> RRID:SCR_024675.
-Version: 3.0.0
-Date: 2024-12-05
+Version: 3.0.0.0001
+Date: 2024-12-06
 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"),
diff --git a/NEWS.md b/NEWS.md
index 4e728b13a..0fbcb4c33 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,16 @@
+# scCustomize 3.X.X (202X-XX-XX)  
+## Added  
+  
+  
+## Changed  
+    
+
+## Fixes  
+  
+
+
+
+
 # scCustomize 3.0.0 (2024-12-05)  
 ## Added  
 **Major Updates to Functionality with rliger Package:**  

From cd9b0a2ee2fdd14fc7a4cce6dc533b4072a304a0 Mon Sep 17 00:00:00 2001
From: samuel-marsh <samuel.marsh@childrens.harvard.edu>
Date: Wed, 11 Dec 2024 07:42:05 -0500
Subject: [PATCH 02/26] fix random downsample

---
 R/Object_Utilities.R | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/R/Object_Utilities.R b/R/Object_Utilities.R
index ae41db644..656373578 100644
--- a/R/Object_Utilities.R
+++ b/R/Object_Utilities.R
@@ -474,7 +474,7 @@ Fetch_Meta.Seurat <- function(
 #' @param num_cells number of cells per ident to use in down-sampling.  This value must be less than or
 #' equal to the size of ident with fewest cells.  Alternatively, can set to "min" which will
 #' use the maximum number of barcodes based on size of smallest group.
-#' @param group.by The ident to use to group cells.  Default is "ident" which use current active.ident.  .
+#' @param group.by The ident to use to group cells.  Default is NULL which use current active.ident.  .
 #' @param return_list logical, whether or not to return the results as list instead of vector, default is
 #' FALSE.
 #' @param allow_lower logical, if number of cells in identity is lower than `num_cells` keep the
@@ -513,7 +513,7 @@ Fetch_Meta.Seurat <- function(
 Random_Cells_Downsample <- function(
     seurat_object,
     num_cells,
-    group.by = "ident",
+    group.by = NULL,
     return_list = FALSE,
     allow_lower = FALSE,
     seed = 123
@@ -522,7 +522,7 @@ Random_Cells_Downsample <- function(
   Is_Seurat(seurat_object = seurat_object)
 
   # set ident in case of NULL
-  group.by <- "ident" %||% group.by
+  group.by <- group.by %||% "ident"
 
   # Check and set idents if not "ident"
   if (group.by != "ident") {
@@ -536,7 +536,7 @@ Random_Cells_Downsample <- function(
     rownames_to_column("barcodes")
 
   # get unique ident vector
-  idents_all <- as.character(levels(x = Idents(object = seurat_object)))
+  idents_all <- as.character(x = levels(x = Idents(object = seurat_object)))
 
   # Find minimum length ident and warn if num_cells not equal or lower
   min_cells <- CellsByIdentities(object = seurat_object)
@@ -574,7 +574,7 @@ Random_Cells_Downsample <- function(
   # set seed and select random cells per ident
   set.seed(seed = seed)
 
-  random_cells <- lapply(1:length(idents_all), function(x) {
+  random_cells <- lapply(1:length(x = idents_all), function(x) {
     clus_barcodes <- cluster_barcodes %>%
       filter(.data[["ident"]] == idents_all[x]) %>%
       column_to_rownames("barcodes") %>%

From ca384b17fb83c8e12ee87dfe9b6c7cffc30c0d87 Mon Sep 17 00:00:00 2001
From: samuel-marsh <samuel.marsh@childrens.harvard.edu>
Date: Wed, 11 Dec 2024 07:42:40 -0500
Subject: [PATCH 03/26] update docs

---
 man/Random_Cells_Downsample.Rd | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/man/Random_Cells_Downsample.Rd b/man/Random_Cells_Downsample.Rd
index 66a452a2c..0ef6d28ea 100644
--- a/man/Random_Cells_Downsample.Rd
+++ b/man/Random_Cells_Downsample.Rd
@@ -7,7 +7,7 @@
 Random_Cells_Downsample(
   seurat_object,
   num_cells,
-  group.by = "ident",
+  group.by = NULL,
   return_list = FALSE,
   allow_lower = FALSE,
   seed = 123
@@ -20,7 +20,7 @@ Random_Cells_Downsample(
 equal to the size of ident with fewest cells.  Alternatively, can set to "min" which will
 use the maximum number of barcodes based on size of smallest group.}
 
-\item{group.by}{The ident to use to group cells.  Default is "ident" which use current active.ident.  .}
+\item{group.by}{The ident to use to group cells.  Default is NULL which use current active.ident.  .}
 
 \item{return_list}{logical, whether or not to return the results as list instead of vector, default is
 FALSE.}

From 6608196bcbd6719effdb8ee4aa407f1dd890220b Mon Sep 17 00:00:00 2001
From: samuel-marsh <samuel.marsh@childrens.harvard.edu>
Date: Wed, 11 Dec 2024 07:42:50 -0500
Subject: [PATCH 04/26] Update changelog

---
 NEWS.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 5e979b246..822711dec 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# scCustomize 3.X.X (202X-XX-XX)  
+# scCustomize 3.0.1 (2024-12-11)  
 ## Added  
   
   
@@ -6,7 +6,7 @@
     
 
 ## Fixes  
-  
+- Fixed bug in `Random_Cells_Downsample` that prevented setting identity using the `group.by` parameter.  
 
 
 

From d36a516316a3bf49789ac31f22cdfa8c614a6445 Mon Sep 17 00:00:00 2001
From: samuel-marsh <samuel.marsh@childrens.harvard.edu>
Date: Wed, 11 Dec 2024 07:42:58 -0500
Subject: [PATCH 05/26] Update cran comments

---
 cran-comments.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cran-comments.md b/cran-comments.md
index 29a557aca..81a17352d 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,5 +1,5 @@
-## Major Update 
-This is major update to version 3.0.0.  See News.md for full changelog.  
+## Hotfix Update 
+This is major update to version 3.0.1.  Fixes bug preventing a function from operating correctly.  See News.md for full changelog.  
 
 
 

From d271f9471f32a3d56072c7637635615f0375ef72 Mon Sep 17 00:00:00 2001
From: samuel-marsh <samuel.marsh@childrens.harvard.edu>
Date: Wed, 11 Dec 2024 07:43:04 -0500
Subject: [PATCH 06/26] bump version and date

---
 DESCRIPTION | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 3f8cf27c6..8c0a16ec9 100644
--- a/DESCRIPTION
+++ b/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> RRID:SCR_024675.
-Version: 3.0.0.0001
-Date: 2024-12-06
+Version: 3.0.1
+Date: 2024-12-11
 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"),

From a70d0646f642ee1aad6db482a4c7b822ddf2bcdf Mon Sep 17 00:00:00 2001
From: samuel-marsh <samuel.marsh@childrens.harvard.edu>
Date: Wed, 11 Dec 2024 15:47:19 -0500
Subject: [PATCH 07/26] fix reduction not setting properly

---
 R/Plotting_Seurat.R | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/R/Plotting_Seurat.R b/R/Plotting_Seurat.R
index 9b4c8d7e9..557a2b38b 100644
--- a/R/Plotting_Seurat.R
+++ b/R/Plotting_Seurat.R
@@ -1688,6 +1688,7 @@ Cell_Highlight_Plot <- function(
                            split.by = split.by,
                            split_seurat = split_seurat,
                            label = label,
+                           reduction = reduction,
                            ...)
 
   # Edit plot legend
@@ -1710,9 +1711,6 @@ Cell_Highlight_Plot <- function(
 }
 
 
-
-
-
 #' DimPlot with modified default settings
 #'
 #' Creates DimPlot with some of the settings modified from their Seurat defaults (colors_use, shuffle, label).

From 78b6d2436b0653d5500b30e4fedae1cc2b61ea32 Mon Sep 17 00:00:00 2001
From: samuel-marsh <samuel.marsh@childrens.harvard.edu>
Date: Wed, 11 Dec 2024 15:50:29 -0500
Subject: [PATCH 08/26] Update changelog

---
 NEWS.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/NEWS.md b/NEWS.md
index 822711dec..95cdf0a3d 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -7,6 +7,7 @@
 
 ## Fixes  
 - Fixed bug in `Random_Cells_Downsample` that prevented setting identity using the `group.by` parameter.  
+- Fixed bug in `Cell_Highlight_Plot` that didn't pass the reduction parameter properly ([#216](https://github.com/samuel-marsh/scCustomize/issues/216)).  
 
 
 

From eb580b470d9dac3a932cf30aa0b55b53ebdbba8a Mon Sep 17 00:00:00 2001
From: samuel-marsh <samuel.marsh@childrens.harvard.edu>
Date: Wed, 11 Dec 2024 15:51:32 -0500
Subject: [PATCH 09/26] fix IEG gene list retrieval

---
 R/Internal_Utilities.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/Internal_Utilities.R b/R/Internal_Utilities.R
index 7de8332fd..e965973a6 100644
--- a/R/Internal_Utilities.R
+++ b/R/Internal_Utilities.R
@@ -827,7 +827,7 @@ Retrieve_IEG_Ensembl_Lists <- function(
 
   # pull lists
   qc_gene_list <- list(
-    ieg = ieg_gene_list[[ieg]]
+    ieg = ensembl_ieg_list[[ieg]]
   )
 
   return(qc_gene_list)

From dbfd77422eb7063838bf4f96eef003540f548ac2 Mon Sep 17 00:00:00 2001
From: samuel-marsh <samuel.marsh@childrens.harvard.edu>
Date: Wed, 11 Dec 2024 15:52:02 -0500
Subject: [PATCH 10/26] Update changelog

---
 NEWS.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/NEWS.md b/NEWS.md
index 95cdf0a3d..f8d77a9a3 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -8,6 +8,7 @@
 ## Fixes  
 - Fixed bug in `Random_Cells_Downsample` that prevented setting identity using the `group.by` parameter.  
 - Fixed bug in `Cell_Highlight_Plot` that didn't pass the reduction parameter properly ([#216](https://github.com/samuel-marsh/scCustomize/issues/216)).  
+- Fixed bug when retrieving ensembl IDs for IEGs.  
 
 
 

From 9c24b3b29a75fa3914a63c015e0beaa5e0e717c8 Mon Sep 17 00:00:00 2001
From: samuel-marsh <samuel.marsh@childrens.harvard.edu>
Date: Thu, 12 Dec 2024 08:10:41 -0500
Subject: [PATCH 11/26] allow return plots without error

---
 R/Plotting_Seurat_Iterative.R | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/R/Plotting_Seurat_Iterative.R b/R/Plotting_Seurat_Iterative.R
index 0f20ee6b6..c4e4f025d 100644
--- a/R/Plotting_Seurat_Iterative.R
+++ b/R/Plotting_Seurat_Iterative.R
@@ -969,12 +969,13 @@ Iterate_FeaturePlot_scCustom <- function(
 
   # Check file_type parameter
   file_type_options <- c(".pdf", ".png", ".tiff", ".jpeg", ".svg")
-  if (is.null(x = file_type)) {
+  if (is.null(x = file_type) && isFALSE(x = return_plots)) {
     cli_abort(message = c("{.code file_type} not specified.",
                           "*" = "Must specify output file type format from the following:",
                           "i" = "{.field {glue_collapse_scCustom(input_string = file_type_options, and = TRUE)}}"))
   }
-  if (!file_type %in% file_type_options) {
+
+  if (!file_type %in% file_type_options && isFALSE(x = return_plots)) {
     cli_abort(message = "{.code file_type} must be one of the following: {.field {glue_collapse_scCustom(input_string = file_type_options, and = TRUE)}}")
   }
 

From d3453c7ba703a270a6c9a4653a970e16c9302cc2 Mon Sep 17 00:00:00 2001
From: samuel-marsh <samuel.marsh@childrens.harvard.edu>
Date: Thu, 12 Dec 2024 08:38:38 -0500
Subject: [PATCH 12/26] edit section title

---
 R/Internal_Utilities.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/Internal_Utilities.R b/R/Internal_Utilities.R
index e965973a6..5f4a028a8 100644
--- a/R/Internal_Utilities.R
+++ b/R/Internal_Utilities.R
@@ -189,7 +189,7 @@ Assay5_Check <- function(
 
 
 #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-#################### WARN/ERROR MESSAGING ####################
+#################### FUNCTION HELPERS  ####################
 #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 

From d001ea787452cfd89c56f1093e613c753075d2ee Mon Sep 17 00:00:00 2001
From: samuel-marsh <samuel.marsh@childrens.harvard.edu>
Date: Thu, 12 Dec 2024 08:39:04 -0500
Subject: [PATCH 13/26] update height/width param for pdf() calls

---
 R/Plotting_Seurat_Iterative.R | 34 ++++++++++++++++++++++++----------
 1 file changed, 24 insertions(+), 10 deletions(-)

diff --git a/R/Plotting_Seurat_Iterative.R b/R/Plotting_Seurat_Iterative.R
index c4e4f025d..3b0682f19 100644
--- a/R/Plotting_Seurat_Iterative.R
+++ b/R/Plotting_Seurat_Iterative.R
@@ -146,6 +146,8 @@ Iterate_DimPlot_bySample <- function(
   file_name = NULL,
   file_type = NULL,
   single_pdf = FALSE,
+  output_width = NULL,
+  output_height = NULL,
   dpi = 600,
   color = "black",
   no_legend = TRUE,
@@ -272,7 +274,7 @@ Iterate_DimPlot_bySample <- function(
       }
       })
     cli_inform(message = "{.field Saving plots to file}")
-    pdf(paste(file_path, file_name, file_type, sep=""))
+    pdf(paste(file_path, file_name, file_type, sep=""), width = output_width, height = output_height)
     pb <- txtProgressBar(min = 0, max = length(all_plots), style = 3, file = stderr())
     for (i in 1:length(all_plots)) {
       print(all_plots[[i]])
@@ -383,6 +385,8 @@ Iterate_Cluster_Highlight_Plot <- function(
     file_name = NULL,
     file_type = NULL,
     single_pdf = FALSE,
+    output_width = NULL,
+    output_height = NULL,
     dpi = 600,
     raster = NULL,
     ...
@@ -468,7 +472,7 @@ Iterate_Cluster_Highlight_Plot <- function(
                                               ...))
     })
     cli_inform(message = "{.field Saving plots to file}")
-    pdf(paste(file_path, file_name, file_type, sep=""))
+    pdf(paste(file_path, file_name, file_type, sep=""), width = output_width, height = output_height)
     pb <- txtProgressBar(min = 0, max = length(all_plots), style = 3, file = stderr())
     for (i in 1:length(all_plots)) {
       print(all_plots[[i]])
@@ -583,6 +587,8 @@ Iterate_Meta_Highlight_Plot <- function(
   file_name = NULL,
   file_type = NULL,
   single_pdf = FALSE,
+  output_width = NULL,
+  output_height = NULL,
   dpi = 600,
   raster = NULL,
   ...
@@ -735,7 +741,7 @@ Iterate_Meta_Highlight_Plot <- function(
 
     })
     cli_inform(message = "{.field Saving plots to file}")
-    pdf(paste(file_path, file_name, file_type, sep=""))
+    pdf(paste(file_path, file_name, file_type, sep=""), width = output_width, height = output_height)
     pb <- txtProgressBar(min = 0, max = length(all_plots), style = 3, file = stderr())
     for (i in 1:length(all_plots)) {
       print(all_plots[[i]])
@@ -888,6 +894,8 @@ Iterate_FeaturePlot_scCustom <- function(
   file_name = NULL,
   file_type = NULL,
   single_pdf = FALSE,
+  output_width = NULL,
+  output_height = NULL,
   features_per_page = 1,
   num_columns = NULL,
   landscape = TRUE,
@@ -1016,7 +1024,7 @@ Iterate_FeaturePlot_scCustom <- function(
       cli_inform(message = "{.field Saving plots to file}")
       # save plots with cluster annotation
       if (!is.null(x = names(x = all_found_features)) && is.null(x = split.by)) {
-        pdf(paste(file_path, file_name, file_type, sep=""))
+        pdf(paste(file_path, file_name, file_type, sep=""), width = output_width, height = output_height)
         pb <- txtProgressBar(min = 0, max = length(all_plots), style = 3, file = stderr())
         for (i in 1:length(all_plots)) {
           print(all_plots[[i]] + ggtitle((paste0(all_found_features[i], "_", names(x = all_found_features)[i]))))
@@ -1026,7 +1034,7 @@ Iterate_FeaturePlot_scCustom <- function(
         dev.off()
       } else {
         # Save plots without cluster annotation
-        pdf(paste(file_path, file_name, file_type, sep=""))
+        pdf(paste(file_path, file_name, file_type, sep=""), width = output_width, height = output_height)
         pb <- txtProgressBar(min = 0, max = length(all_plots), style = 3, file = stderr())
         for (i in 1:length(all_plots)) {
           print(all_plots[[i]])
@@ -1227,6 +1235,8 @@ Iterate_VlnPlot_scCustom <- function(
   file_name = NULL,
   file_type = NULL,
   single_pdf = FALSE,
+  output_width = NULL,
+  output_height = NULL,
   raster = NULL,
   dpi = 600,
   ggplot_default_colors = FALSE,
@@ -1320,7 +1330,7 @@ Iterate_VlnPlot_scCustom <- function(
     pboptions(char = "=")
     all_plots <- pblapply(all_found_features,function(gene) {VlnPlot_scCustom(seurat_object = seurat_object, features = gene, colors_use = colors_use, pt.size = pt.size, group.by = group.by, raster = raster, ggplot_default_colors = ggplot_default_colors, color_seed = color_seed, split.by = split.by, ...)})
     cli_inform(message = "{.field Saving plots to file}")
-    pdf(paste(file_path, file_name, file_type, sep=""))
+    pdf(paste(file_path, file_name, file_type, sep=""), width = output_width, height = output_height)
     pb <- txtProgressBar(min = 0, max = length(all_plots), style = 3, file = stderr())
     for (i in 1:length(all_plots)) {
       print(all_plots[[i]])
@@ -1406,6 +1416,8 @@ Iterate_Plot_Density_Custom <- function(
   file_name = NULL,
   file_type = NULL,
   single_pdf = FALSE,
+  output_width = NULL,
+  output_height = NULL,
   dpi = 600,
   reduction = NULL,
   combine = TRUE,
@@ -1499,7 +1511,7 @@ Iterate_Plot_Density_Custom <- function(
     cli_inform(message = "{.field Saving plots to file}")
     # save plots with cluster annotation
     if (!is.null(x = names(x = gene_list))) {
-      pdf(paste(file_path, file_name, file_type, sep=""))
+      pdf(paste(file_path, file_name, file_type, sep=""), width = output_width, height = output_height)
       pb <- txtProgressBar(min = 0, max = length(all_plots), style = 3, file = stderr())
       for (i in 1:length(all_plots)) {
         print(all_plots[[i]] + ggtitle((paste0(gene_list[i], "_", names(x = gene_list)[i]))))
@@ -1509,7 +1521,7 @@ Iterate_Plot_Density_Custom <- function(
       dev.off()
     } else {
       # Save plots without cluster annotation
-      pdf(paste(file_path, file_name, file_type, sep=""))
+      pdf(paste(file_path, file_name, file_type, sep=""), width = output_width, height = output_height)
       pb <- txtProgressBar(min = 0, max = length(all_plots), style = 3, file = stderr())
       for (i in 1:length(all_plots)) {
         print(all_plots[[i]])
@@ -1607,6 +1619,8 @@ Iterate_Plot_Density_Joint <- function(
   file_name = NULL,
   file_type = NULL,
   single_pdf = FALSE,
+  output_width = NULL,
+  output_height = NULL,
   dpi = 600,
   reduction = NULL,
   combine = TRUE,
@@ -1725,7 +1739,7 @@ Iterate_Plot_Density_Joint <- function(
     cli_inform(message = "{.field Saving plots to file}")
     # save plots with cluster annotation
     if (!is.null(x = names(x = final_gene_list))) {
-      pdf(paste(file_path, file_name, file_type, sep=""))
+      pdf(paste(file_path, file_name, file_type, sep=""), width = output_width, height = output_height)
       pb <- txtProgressBar(min = 0, max = length(all_plots), style = 3, file = stderr())
       for (i in 1:length(all_plots)) {
         print(all_plots[[i]] + ggtitle((paste0(paste(final_gene_list[[i]], collapse = "_"), "_", names(x = final_gene_list)[i]))))
@@ -1735,7 +1749,7 @@ Iterate_Plot_Density_Joint <- function(
       dev.off()
     } else {
       # Save plots without cluster annotation
-      pdf(paste(file_path, file_name, file_type, sep=""))
+      pdf(paste(file_path, file_name, file_type, sep=""), width = output_width, height = output_height)
       pb <- txtProgressBar(min = 0, max = length(all_plots), style = 3, file = stderr())
       for (i in 1:length(all_plots)) {
         print(all_plots[[i]])

From 43a8bb897fc79ea21d8ec62a9b31a7d22215764a Mon Sep 17 00:00:00 2001
From: samuel-marsh <samuel.marsh@childrens.harvard.edu>
Date: Thu, 12 Dec 2024 08:48:59 -0500
Subject: [PATCH 14/26] reorg and add replace_null internal function

---
 R/Internal_Utilities.R | 153 ++++++++++++++++++++++++-----------------
 1 file changed, 91 insertions(+), 62 deletions(-)

diff --git a/R/Internal_Utilities.R b/R/Internal_Utilities.R
index 5f4a028a8..63d51e772 100644
--- a/R/Internal_Utilities.R
+++ b/R/Internal_Utilities.R
@@ -47,7 +47,7 @@
 
 
 #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-#################### Object Checks ####################
+#################### Object/Feature Checks ####################
 #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 
@@ -188,8 +188,68 @@ Assay5_Check <- function(
 }
 
 
+#' Perform Feature and Meta Checks before plotting
+#'
+#' Wraps the `Feature_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.
+#' @param assay Assay to use (default all assays present).
+#'
+#' @return vector of features and/or meta data that were found in object.
+#'
+#' @noRd
+#'
+#' @keywords internal
+#'
+
+Feature_PreCheck <- function(
+    object,
+    features,
+    assay = NULL
+) {
+  # set assay (if null set to active assay)
+  assay <- assay %||% Assays(object = object)
+
+  # Check features and meta to determine which features present
+  features_list <- Feature_Present(data = object, features = features, omit_warn = FALSE, print_msg = FALSE, case_check_msg = FALSE, return_none = TRUE, seurat_assay = assay)
+
+  meta_list <- Meta_Present(object = object, meta_col_names = features_list[[2]], omit_warn = FALSE, print_msg = FALSE, return_none = TRUE)
+
+  reduction_list <- Reduction_Loading_Present(seurat_object = object, reduction_names = meta_list[[2]], omit_warn = FALSE, print_msg = FALSE, return_none = TRUE)
+
+  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) {
+    cli_abort(message = c("No features were found.",
+                          "*" = "The following are not present in object:",
+                          "i" = "{.field {glue_collapse_scCustom(input_string = all_not_found_features, and = TRUE)}}")
+    )
+  }
+
+  # Return message of features not found
+  if (length(x = all_not_found_features) > 0) {
+    op <- options(warn = 1)
+    on.exit(options(op))
+    cli_warn(message = c("The following features were omitted as they were not found:",
+                         "i" = "{.field {glue_collapse_scCustom(input_string = all_not_found_features, and = TRUE)}}")
+    )
+  }
+
+  # Check feature case and message if found
+  Case_Check(seurat_object = object, gene_list = all_not_found_features, case_check_msg = TRUE, return_features = FALSE)
+
+  # return all found features
+  return(all_found_features)
+}
+
+
 #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-#################### FUNCTION HELPERS  ####################
+#################### FUNCTION HELPERS ####################
 #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 
@@ -250,66 +310,6 @@ glue_collapse_scCustom <- function(
 }
 
 
-#' Perform Feature and Meta Checks before plotting
-#'
-#' Wraps the `Feature_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.
-#' @param assay Assay to use (default all assays present).
-#'
-#' @return vector of features and/or meta data that were found in object.
-#'
-#' @noRd
-#'
-#' @keywords internal
-#'
-
-Feature_PreCheck <- function(
-    object,
-    features,
-    assay = NULL
-) {
-  # set assay (if null set to active assay)
-  assay <- assay %||% Assays(object = object)
-
-  # Check features and meta to determine which features present
-  features_list <- Feature_Present(data = object, features = features, omit_warn = FALSE, print_msg = FALSE, case_check_msg = FALSE, return_none = TRUE, seurat_assay = assay)
-
-  meta_list <- Meta_Present(object = object, meta_col_names = features_list[[2]], omit_warn = FALSE, print_msg = FALSE, return_none = TRUE)
-
-  reduction_list <- Reduction_Loading_Present(seurat_object = object, reduction_names = meta_list[[2]], omit_warn = FALSE, print_msg = FALSE, return_none = TRUE)
-
-  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) {
-    cli_abort(message = c("No features were found.",
-                          "*" = "The following are not present in object:",
-                          "i" = "{.field {glue_collapse_scCustom(input_string = all_not_found_features, and = TRUE)}}")
-    )
-  }
-
-  # Return message of features not found
-  if (length(x = all_not_found_features) > 0) {
-    op <- options(warn = 1)
-    on.exit(options(op))
-    cli_warn(message = c("The following features were omitted as they were not found:",
-                         "i" = "{.field {glue_collapse_scCustom(input_string = all_not_found_features, and = TRUE)}}")
-    )
-  }
-
-  # Check feature case and message if found
-  Case_Check(seurat_object = object, gene_list = all_not_found_features, case_check_msg = TRUE, return_features = FALSE)
-
-  # return all found features
-  return(all_found_features)
-}
-
-
 #' Ask yes/no question to proceed
 #'
 #' Asks the user to answer yes/no question and returns logical value depending on
@@ -337,6 +337,35 @@ yesno <- function(msg, .envir = parent.frame()) {
 }
 
 
+#' Change function parameter value from NULL to NA
+#'
+#' Provides method to change parameter value dynamically within function to suit defaults of other functions.
+#' Used in iterative plotting functions.
+#'
+#' @return if NULL returns NA otherwise returns input value.
+#'
+#'
+#' @import cli
+#'
+#' @noRd
+#'
+
+replace_null <- function(
+    parameter
+) {
+  # check length
+  if (length(x = parameter) > 1) {
+    cli_abort(message = "{.code parameter} must be single value.")
+  }
+
+  # check NULL and swap NA
+  if (is.null(x = parameter)) {
+    parameter <- NA
+  }
+  return(parameter)
+}
+
+
 #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 #################### QC HELPERS ####################
 #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

From cccf3b07f1951eb095090aa7daae36569093d6f2 Mon Sep 17 00:00:00 2001
From: samuel-marsh <samuel.marsh@childrens.harvard.edu>
Date: Thu, 12 Dec 2024 08:50:34 -0500
Subject: [PATCH 15/26] update documentation

---
 R/Internal_Utilities.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/R/Internal_Utilities.R b/R/Internal_Utilities.R
index 63d51e772..bf205989c 100644
--- a/R/Internal_Utilities.R
+++ b/R/Internal_Utilities.R
@@ -342,6 +342,8 @@ yesno <- function(msg, .envir = parent.frame()) {
 #' Provides method to change parameter value dynamically within function to suit defaults of other functions.
 #' Used in iterative plotting functions.
 #'
+#' @param parameter the parameter to check for NULL
+#'
 #' @return if NULL returns NA otherwise returns input value.
 #'
 #'

From 076345fb1d60a6ca585cc39646a3b0e77b82eba4 Mon Sep 17 00:00:00 2001
From: samuel-marsh <samuel.marsh@childrens.harvard.edu>
Date: Thu, 12 Dec 2024 08:54:35 -0500
Subject: [PATCH 16/26] update ggsave calls for height/width params

---
 R/Plotting_Seurat_Iterative.R | 40 +++++++++++++++++------------------
 1 file changed, 20 insertions(+), 20 deletions(-)

diff --git a/R/Plotting_Seurat_Iterative.R b/R/Plotting_Seurat_Iterative.R
index 3b0682f19..baa488c58 100644
--- a/R/Plotting_Seurat_Iterative.R
+++ b/R/Plotting_Seurat_Iterative.R
@@ -301,7 +301,7 @@ Iterate_DimPlot_bySample <- function(
             xlim(x_axis) +
             ylim(y_axis)
         }
-        suppressMessages(ggsave(filename = paste(file_path, column_list[[i]], file_name, file_type, sep=""), dpi = dpi))
+        suppressMessages(ggsave(filename = paste(file_path, column_list[[i]], file_name, file_type, sep=""), dpi = dpi, height = replace_null(parameter = output_height), width = replace_null(parameter = output_width)))
         setTxtProgressBar(pb = pb, value = i)
         }
       close(con = pb)
@@ -323,7 +323,7 @@ Iterate_DimPlot_bySample <- function(
             xlim(x_axis) +
             ylim(y_axis)
         }
-        suppressMessages(ggsave(filename = paste(file_path, column_list[[i]], file_name, file_type, sep=""), useDingbats = FALSE))
+        suppressMessages(ggsave(filename = paste(file_path, column_list[[i]], file_name, file_type, sep=""), useDingbats = FALSE, height = replace_null(parameter = output_height), width = replace_null(parameter = output_width)))
         setTxtProgressBar(pb = pb, value = i)
         }
       close(con = pb)
@@ -495,7 +495,7 @@ Iterate_Cluster_Highlight_Plot <- function(
                                                 reduction = reduction,
                                                 raster = raster,
                                                 ...))
-        suppressMessages(ggsave(filename = paste(file_path, list_idents_save[i], "_", file_name, file_type, sep=""), dpi = dpi))
+        suppressMessages(ggsave(filename = paste(file_path, list_idents_save[i], "_", file_name, file_type, sep=""), dpi = dpi, height = replace_null(parameter = output_height), width = replace_null(parameter = output_width)))
         setTxtProgressBar(pb = pb, value = i)
       }
       close(con = pb)
@@ -513,7 +513,7 @@ Iterate_Cluster_Highlight_Plot <- function(
                                                 reduction = reduction,
                                                 raster = raster,
                                                 ...))
-        suppressMessages(ggsave(filename = paste(file_path, list_idents_save[[i]], "_", file_name, file_type, sep=""), useDingbats = FALSE))
+        suppressMessages(ggsave(filename = paste(file_path, list_idents_save[[i]], "_", file_name, file_type, sep=""), useDingbats = FALSE, height = replace_null(parameter = output_height), width = replace_null(parameter = output_width)))
         setTxtProgressBar(pb = pb, value = i)
       }
       close(con = pb)
@@ -781,7 +781,7 @@ Iterate_Meta_Highlight_Plot <- function(
                                                ...))
         }
 
-        suppressMessages(ggsave(filename = paste(file_path, list_idents_save[i], "_", file_name, file_type, sep=""), dpi = dpi))
+        suppressMessages(ggsave(filename = paste(file_path, list_idents_save[i], "_", file_name, file_type, sep=""), dpi = dpi, height = replace_null(parameter = output_height), width = replace_null(parameter = output_width)))
         setTxtProgressBar(pb = pb, value = i)
       }
       close(con = pb)
@@ -816,7 +816,7 @@ Iterate_Meta_Highlight_Plot <- function(
                                                ...))
         }
 
-        suppressMessages(ggsave(filename = paste(file_path, list_idents_save[[i]], "_", file_name, file_type, sep=""), useDingbats = FALSE))
+        suppressMessages(ggsave(filename = paste(file_path, list_idents_save[[i]], "_", file_name, file_type, sep=""), useDingbats = FALSE, height = replace_null(parameter = output_height), width = replace_null(parameter = output_width)))
         setTxtProgressBar(pb = pb, value = i)
       }
       close(con = pb)
@@ -1139,9 +1139,9 @@ Iterate_FeaturePlot_scCustom <- function(
       for (i in 1:length(all_found_features)) {
         FeaturePlot_scCustom(seurat_object = seurat_object, features = all_found_features[i], colors_use = colors_use, na_color = na_color, na_cutoff = na_cutoff, split.by = split.by, order = order, pt.size = pt.size, reduction = reduction, raster = raster, alpha_exp = alpha_exp, alpha_na_exp = alpha_na_exp, ...)
         if (!is.null(x = names(x = all_found_features))) {
-          suppressMessages(ggsave(filename = paste(file_path, all_found_features[i], "_", names(x = all_found_features)[i], "_", file_name, file_type, sep=""), dpi = dpi))
+          suppressMessages(ggsave(filename = paste(file_path, all_found_features[i], "_", names(x = all_found_features)[i], "_", file_name, file_type, sep=""), dpi = dpi, height = replace_null(parameter = output_height), width = replace_null(parameter = output_width)))
         } else {
-          suppressMessages(ggsave(filename = paste(file_path, all_found_features[i], "_", file_name, file_type, sep=""), dpi = dpi))
+          suppressMessages(ggsave(filename = paste(file_path, all_found_features[i], "_", file_name, file_type, sep=""), dpi = dpi, height = replace_null(parameter = output_height), width = replace_null(parameter = output_width)))
         }
         setTxtProgressBar(pb = pb, value = i)
       }
@@ -1153,9 +1153,9 @@ Iterate_FeaturePlot_scCustom <- function(
       for (i in 1:length(all_found_features)) {
         FeaturePlot_scCustom(seurat_object = seurat_object, features = all_found_features[i], colors_use = colors_use, na_color = na_color, na_cutoff = na_cutoff, split.by = split.by, order = order, pt.size = pt.size, reduction = reduction, raster = raster, alpha_exp = alpha_exp, alpha_na_exp = alpha_na_exp, ...)
         if (!is.null(x = names(x = all_found_features))) {
-          suppressMessages(ggsave(filename = paste(file_path, all_found_features[i], "_", names(x = all_found_features)[i], "_", file_name, file_type, sep=""), useDingbats = FALSE))
+          suppressMessages(ggsave(filename = paste(file_path, all_found_features[i], "_", names(x = all_found_features)[i], "_", file_name, file_type, sep=""), useDingbats = FALSE, height = replace_null(parameter = output_height), width = replace_null(parameter = output_width)))
         } else {
-          suppressMessages(ggsave(filename = paste(file_path, all_found_features[i], "_", file_name, file_type, sep=""), useDingbats = FALSE))
+          suppressMessages(ggsave(filename = paste(file_path, all_found_features[i], "_", file_name, file_type, sep=""), useDingbats = FALSE, height = replace_null(parameter = output_height), width = replace_null(parameter = output_width)))
         }
         setTxtProgressBar(pb = pb, value = i)
       }
@@ -1345,7 +1345,7 @@ Iterate_VlnPlot_scCustom <- function(
       pb <- txtProgressBar(min = 0, max = length(x = all_found_features), style = 3, file = stderr())
       for (i in 1:length(x = all_found_features)) {
         VlnPlot_scCustom(seurat_object = seurat_object, features = all_found_features[i], colors_use = colors_use, pt.size = pt.size, group.by = group.by, raster = raster, ggplot_default_colors = ggplot_default_colors, color_seed = color_seed, split.by = split.by, ...)
-        suppressMessages(ggsave(filename = paste(file_path, all_found_features[i], file_name, file_type, sep=""), dpi = dpi))
+        suppressMessages(ggsave(filename = paste(file_path, all_found_features[i], file_name, file_type, sep=""), dpi = dpi, height = replace_null(parameter = output_height), width = replace_null(parameter = output_width)))
         setTxtProgressBar(pb = pb, value = i)
       }
       close(con = pb)
@@ -1355,7 +1355,7 @@ Iterate_VlnPlot_scCustom <- function(
       pb <- txtProgressBar(min = 0, max = length(x = all_found_features), style = 3, file = stderr())
       for (i in 1:length(x = all_found_features)) {
         VlnPlot_scCustom(seurat_object = seurat_object, features = all_found_features[i], colors_use = colors_use, pt.size = pt.size, group.by = group.by, raster = raster, ggplot_default_colors = ggplot_default_colors, color_seed = color_seed, split.by = split.by, ...)
-        suppressMessages(ggsave(filename = paste(file_path, all_found_features[i], file_name, file_type, sep=""), useDingbats = FALSE))
+        suppressMessages(ggsave(filename = paste(file_path, all_found_features[i], file_name, file_type, sep=""), useDingbats = FALSE, height = replace_null(parameter = output_height), width = replace_null(parameter = output_width)))
         setTxtProgressBar(pb = pb, value = i)
       }
       close(con = pb)
@@ -1538,9 +1538,9 @@ Iterate_Plot_Density_Custom <- function(
       for (i in 1:length(gene_list)) {
         Plot_Density_Custom(seurat_object = seurat_object, features = gene_list[i], joint = FALSE, viridis_palette = viridis_palette, custom_palette = custom_palette, pt.size = pt.size, reduction = reduction, ...)
         if (!is.null(x = names(x = gene_list))) {
-          suppressMessages(ggsave(filename = paste(file_path, gene_list[i], "_", names(x = gene_list)[i], "_", file_name, file_type, sep=""), dpi = dpi))
+          suppressMessages(ggsave(filename = paste(file_path, gene_list[i], "_", names(x = gene_list)[i], "_", file_name, file_type, sep=""), dpi = dpi, height = replace_null(parameter = output_height), width = replace_null(parameter = output_width)))
         } else {
-          suppressMessages(ggsave(filename = paste(file_path, gene_list[i], "_", file_name, file_type, sep=""), dpi = dpi))
+          suppressMessages(ggsave(filename = paste(file_path, gene_list[i], "_", file_name, file_type, sep=""), dpi = dpi, height = replace_null(parameter = output_height), width = replace_null(parameter = output_width)))
         }
         setTxtProgressBar(pb = pb, value = i)
       }
@@ -1552,9 +1552,9 @@ Iterate_Plot_Density_Custom <- function(
       for (i in 1:length(gene_list)) {
         Plot_Density_Custom(seurat_object = seurat_object, features = gene_list[i], joint = FALSE, viridis_palette = viridis_palette, custom_palette = custom_palette, pt.size = pt.size, reduction = reduction, ...)
         if (!is.null(x = names(x = gene_list))) {
-          suppressMessages(ggsave(filename = paste(file_path, gene_list[i], "_", names(x = gene_list)[i], "_", file_name, file_type, sep=""), useDingbats = FALSE))
+          suppressMessages(ggsave(filename = paste(file_path, gene_list[i], "_", names(x = gene_list)[i], "_", file_name, file_type, sep=""), useDingbats = FALSE, height = replace_null(parameter = output_height), width = replace_null(parameter = output_width)))
         } else {
-          suppressMessages(ggsave(filename = paste(file_path, gene_list[i], "_", file_name, file_type, sep=""), useDingbats = FALSE))
+          suppressMessages(ggsave(filename = paste(file_path, gene_list[i], "_", file_name, file_type, sep=""), useDingbats = FALSE, height = replace_null(parameter = output_height), width = replace_null(parameter = output_width)))
         }
         setTxtProgressBar(pb = pb, value = i)
       }
@@ -1766,9 +1766,9 @@ Iterate_Plot_Density_Joint <- function(
       for (i in 1:length(final_gene_list)) {
         Plot_Density_Joint_Only(seurat_object = seurat_object, features = final_gene_list[[i]], viridis_palette = viridis_palette, custom_palette = custom_palette, pt.size = pt.size, reduction = reduction, ...)
         if (!is.null(x = names(x = final_gene_list))) {
-          suppressMessages(ggsave(filename = paste(file_path, paste(final_gene_list[[i]], collapse = "_"), "_", names(x = final_gene_list)[i], "_", file_name, file_type, sep=""), dpi = dpi))
+          suppressMessages(ggsave(filename = paste(file_path, paste(final_gene_list[[i]], collapse = "_"), "_", names(x = final_gene_list)[i], "_", file_name, file_type, sep=""), dpi = dpi, height = replace_null(parameter = output_height), width = replace_null(parameter = output_width)))
         } else {
-          suppressMessages(ggsave(filename = paste(file_path, paste(final_gene_list[[i]], collapse = "_"), "_", file_name, file_type, sep=""), dpi = dpi))
+          suppressMessages(ggsave(filename = paste(file_path, paste(final_gene_list[[i]], collapse = "_"), "_", file_name, file_type, sep=""), dpi = dpi, height = replace_null(parameter = output_height), width = replace_null(parameter = output_width)))
         }
         setTxtProgressBar(pb = pb, value = i)
       }
@@ -1780,9 +1780,9 @@ Iterate_Plot_Density_Joint <- function(
       for (i in 1:length(final_gene_list)) {
         Plot_Density_Joint_Only(seurat_object = seurat_object, features = final_gene_list[[i]], viridis_palette = viridis_palette, custom_palette = custom_palette, pt.size = pt.size, reduction = reduction, ...)
         if (!is.null(x = names(x = final_gene_list))) {
-          suppressMessages(ggsave(filename = paste(file_path, paste(final_gene_list[[i]], collapse = "_"), "_", names(x = final_gene_list)[i], "_", file_name, file_type, sep=""), useDingbats = FALSE))
+          suppressMessages(ggsave(filename = paste(file_path, paste(final_gene_list[[i]], collapse = "_"), "_", names(x = final_gene_list)[i], "_", file_name, file_type, sep=""), useDingbats = FALSE, height = replace_null(parameter = output_height), width = replace_null(parameter = output_width)))
         } else {
-          suppressMessages(ggsave(filename = paste(file_path, paste(final_gene_list[[i]], collapse = "_"), "_", file_name, file_type, sep=""), useDingbats = FALSE))
+          suppressMessages(ggsave(filename = paste(file_path, paste(final_gene_list[[i]], collapse = "_"), "_", file_name, file_type, sep=""), useDingbats = FALSE, height = replace_null(parameter = output_height), width = replace_null(parameter = output_width)))
         }
         setTxtProgressBar(pb = pb, value = i)
       }

From 0d386e2ece0aa105554e6581caee0b1b276c94aa Mon Sep 17 00:00:00 2001
From: samuel-marsh <samuel.marsh@childrens.harvard.edu>
Date: Thu, 12 Dec 2024 08:57:27 -0500
Subject: [PATCH 17/26] update manual entries

---
 R/Plotting_Seurat_Iterative.R | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/R/Plotting_Seurat_Iterative.R b/R/Plotting_Seurat_Iterative.R
index baa488c58..06c336129 100644
--- a/R/Plotting_Seurat_Iterative.R
+++ b/R/Plotting_Seurat_Iterative.R
@@ -103,6 +103,8 @@ Iterate_PC_Loading_Plots <- function(
 #' @param file_name name suffix to append after sample name.
 #' @param file_type File type to save output as.  Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".
 #' @param single_pdf saves all plots to single PDF file (default = FALSE).  `file_type`` must be .pdf
+#' @param output_width the width (in inches) for output page size.  Default is NULL.
+#' @param output_height the height (in inches) for output page size.  Default is NULL.
 #' @param color color scheme to use.
 #' @param no_legend logical, whether or not to include plot legend, default is TRUE.
 #' @param title_prefix Value that should be used for plot title prefix if `no_legend = TRUE`.
@@ -346,7 +348,9 @@ Iterate_DimPlot_bySample <- function(
 #' @param file_path directory file path and/or file name prefix.  Defaults to current wd.
 #' @param file_name name suffix to append after sample name.
 #' @param file_type File type to save output as.  Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".
-#' @param single_pdf saves all plots to single PDF file (default = FALSE).  `file_type`` must be .pdf
+#' @param single_pdf saves all plots to single PDF file (default = FALSE).  `file_type`` must be .pdf.
+#' @param output_width the width (in inches) for output page size.  Default is NULL.
+#' @param output_height the height (in inches) for output page size.  Default is NULL.
 #' @param dpi dpi for image saving.
 #' @param raster Convert points to raster format.  Default is NULL which will rasterize by default if
 #' greater than 200,000 cells.
@@ -542,7 +546,9 @@ Iterate_Cluster_Highlight_Plot <- function(
 #' @param file_path directory file path and/or file name prefix.  Defaults to current wd.
 #' @param file_name name suffix to append after sample name.
 #' @param file_type File type to save output as.  Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".
-#' @param single_pdf saves all plots to single PDF file (default = FALSE).  `file_type`` must be .pdf
+#' @param single_pdf saves all plots to single PDF file (default = FALSE).  `file_type`` must be .pdf.
+#' @param output_width the width (in inches) for output page size.  Default is NULL.
+#' @param output_height the height (in inches) for output page size.  Default is NULL.
 #' @param dpi dpi for image saving.
 #' @param raster Convert points to raster format.  Default is NULL which will rasterize by default if
 #' greater than 200,000 cells.
@@ -842,6 +848,8 @@ Iterate_Meta_Highlight_Plot <- function(
 #' @param file_name name suffix and file extension.
 #' @param file_type File type to save output as.  Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".
 #' @param single_pdf saves all plots to single PDF file (default = FALSE).
+#' @param output_width the width (in inches) for output page size.  Default is NULL.
+#' @param output_height the height (in inches) for output page size.  Default is NULL.
 #' @param features_per_page numeric, number of features to plot on single page if `single_pdf = TRUE`.  Default is 1.
 #' @param num_columns Number of columns in plot layout (only applicable if `single_pdf = TRUE` AND
 #' `features_per_page` > 1).
@@ -1194,6 +1202,8 @@ Iterate_FeaturePlot_scCustom <- function(
 #' @param file_name name suffix and file extension.
 #' @param file_type File type to save output as.  Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".
 #' @param single_pdf saves all plots to single PDF file (default = FALSE).  `file_type`` must be .pdf.
+#' @param output_width the width (in inches) for output page size.  Default is NULL.
+#' @param output_height the height (in inches) for output page size.  Default is NULL.
 #' @param raster Convert points to raster format.  Default is NULL which will rasterize by default if
 #' greater than 100,000 total points plotted (# Cells x # of features).
 #' @param dpi dpi for image saving.
@@ -1378,6 +1388,8 @@ Iterate_VlnPlot_scCustom <- function(
 #' @param file_name name suffix and file extension.
 #' @param file_type File type to save output as.  Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".
 #' @param single_pdf saves all plots to single PDF file (default = FALSE).  `file_type`` must be .pdf.
+#' @param output_width the width (in inches) for output page size.  Default is NULL.
+#' @param output_height the height (in inches) for output page size.  Default is NULL.
 #' @param dpi dpi for image saving.
 #' @param reduction Dimensionality Reduction to use (if NULL then defaults to Object default)
 #' @param joint NULL.  This function only supports `joint = FALSE`.  Leave as NULL to generate plots.  To iterate joint plots see function: `Iterate_Plot_Density_Joint`.
@@ -1580,6 +1592,8 @@ Iterate_Plot_Density_Custom <- function(
 #' @param file_name name suffix and file extension.
 #' @param file_type File type to save output as.  Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".
 #' @param single_pdf saves all plots to single PDF file (default = FALSE).  `file_type`` must be .pdf.
+#' @param output_width the width (in inches) for output page size.  Default is NULL.
+#' @param output_height the height (in inches) for output page size.  Default is NULL.
 #' @param dpi dpi for image saving.
 #' @param reduction Dimensionality Reduction to use (if NULL then defaults to Object default)
 #' @param joint NULL.  This function only supports `joint = FALSE`.  Leave as NULL to generate plots.  To iterate joint plots see function: `Iterate_Plot_Density_Joint`.

From 9eb2d5613008166c1ee696beadddeac212f63f1e Mon Sep 17 00:00:00 2001
From: samuel-marsh <samuel.marsh@childrens.harvard.edu>
Date: Thu, 12 Dec 2024 08:57:41 -0500
Subject: [PATCH 18/26] Update docs

---
 man/Iterate_Cluster_Highlight_Plot.Rd | 8 +++++++-
 man/Iterate_DimPlot_bySample.Rd       | 6 ++++++
 man/Iterate_FeaturePlot_scCustom.Rd   | 6 ++++++
 man/Iterate_Meta_Highlight_Plot.Rd    | 8 +++++++-
 man/Iterate_Plot_Density_Custom.Rd    | 6 ++++++
 man/Iterate_Plot_Density_Joint.Rd     | 6 ++++++
 man/Iterate_VlnPlot_scCustom.Rd       | 6 ++++++
 7 files changed, 44 insertions(+), 2 deletions(-)

diff --git a/man/Iterate_Cluster_Highlight_Plot.Rd b/man/Iterate_Cluster_Highlight_Plot.Rd
index dc00ae7c6..ca76a0cff 100644
--- a/man/Iterate_Cluster_Highlight_Plot.Rd
+++ b/man/Iterate_Cluster_Highlight_Plot.Rd
@@ -14,6 +14,8 @@ Iterate_Cluster_Highlight_Plot(
   file_name = NULL,
   file_type = NULL,
   single_pdf = FALSE,
+  output_width = NULL,
+  output_height = NULL,
   dpi = 600,
   raster = NULL,
   ...
@@ -37,7 +39,11 @@ all clusters/plots or a vector of colors equal to the number of clusters to use
 
 \item{file_type}{File type to save output as.  Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".}
 
-\item{single_pdf}{saves all plots to single PDF file (default = FALSE).  `file_type`` must be .pdf}
+\item{single_pdf}{saves all plots to single PDF file (default = FALSE).  `file_type`` must be .pdf.}
+
+\item{output_width}{the width (in inches) for output page size.  Default is NULL.}
+
+\item{output_height}{the height (in inches) for output page size.  Default is NULL.}
 
 \item{dpi}{dpi for image saving.}
 
diff --git a/man/Iterate_DimPlot_bySample.Rd b/man/Iterate_DimPlot_bySample.Rd
index a87595aca..7ca4b054c 100644
--- a/man/Iterate_DimPlot_bySample.Rd
+++ b/man/Iterate_DimPlot_bySample.Rd
@@ -11,6 +11,8 @@ Iterate_DimPlot_bySample(
   file_name = NULL,
   file_type = NULL,
   single_pdf = FALSE,
+  output_width = NULL,
+  output_height = NULL,
   dpi = 600,
   color = "black",
   no_legend = TRUE,
@@ -35,6 +37,10 @@ Iterate_DimPlot_bySample(
 
 \item{single_pdf}{saves all plots to single PDF file (default = FALSE).  `file_type`` must be .pdf}
 
+\item{output_width}{the width (in inches) for output page size.  Default is NULL.}
+
+\item{output_height}{the height (in inches) for output page size.  Default is NULL.}
+
 \item{dpi}{dpi for image saving.}
 
 \item{color}{color scheme to use.}
diff --git a/man/Iterate_FeaturePlot_scCustom.Rd b/man/Iterate_FeaturePlot_scCustom.Rd
index 3efa5b61b..9eeb9fa7f 100644
--- a/man/Iterate_FeaturePlot_scCustom.Rd
+++ b/man/Iterate_FeaturePlot_scCustom.Rd
@@ -17,6 +17,8 @@ Iterate_FeaturePlot_scCustom(
   file_name = NULL,
   file_type = NULL,
   single_pdf = FALSE,
+  output_width = NULL,
+  output_height = NULL,
   features_per_page = 1,
   num_columns = NULL,
   landscape = TRUE,
@@ -55,6 +57,10 @@ will be incorporated into plot title if \code{single_pdf = TRUE} or into file na
 
 \item{single_pdf}{saves all plots to single PDF file (default = FALSE).}
 
+\item{output_width}{the width (in inches) for output page size.  Default is NULL.}
+
+\item{output_height}{the height (in inches) for output page size.  Default is NULL.}
+
 \item{features_per_page}{numeric, number of features to plot on single page if \code{single_pdf = TRUE}.  Default is 1.}
 
 \item{num_columns}{Number of columns in plot layout (only applicable if \code{single_pdf = TRUE} AND
diff --git a/man/Iterate_Meta_Highlight_Plot.Rd b/man/Iterate_Meta_Highlight_Plot.Rd
index 4f285aa0d..a4179008d 100644
--- a/man/Iterate_Meta_Highlight_Plot.Rd
+++ b/man/Iterate_Meta_Highlight_Plot.Rd
@@ -19,6 +19,8 @@ Iterate_Meta_Highlight_Plot(
   file_name = NULL,
   file_type = NULL,
   single_pdf = FALSE,
+  output_width = NULL,
+  output_height = NULL,
   dpi = 600,
   raster = NULL,
   ...
@@ -54,7 +56,11 @@ If NULL the value of \code{meta_data_column} will be used.  Default is NULL.}
 
 \item{file_type}{File type to save output as.  Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".}
 
-\item{single_pdf}{saves all plots to single PDF file (default = FALSE).  `file_type`` must be .pdf}
+\item{single_pdf}{saves all plots to single PDF file (default = FALSE).  `file_type`` must be .pdf.}
+
+\item{output_width}{the width (in inches) for output page size.  Default is NULL.}
+
+\item{output_height}{the height (in inches) for output page size.  Default is NULL.}
 
 \item{dpi}{dpi for image saving.}
 
diff --git a/man/Iterate_Plot_Density_Custom.Rd b/man/Iterate_Plot_Density_Custom.Rd
index 4b2029ac5..1fb6c95dd 100644
--- a/man/Iterate_Plot_Density_Custom.Rd
+++ b/man/Iterate_Plot_Density_Custom.Rd
@@ -14,6 +14,8 @@ Iterate_Plot_Density_Custom(
   file_name = NULL,
   file_type = NULL,
   single_pdf = FALSE,
+  output_width = NULL,
+  output_height = NULL,
   dpi = 600,
   reduction = NULL,
   combine = TRUE,
@@ -41,6 +43,10 @@ will be incorporated into plot title if \code{single_pdf = TRUE} or into file na
 
 \item{single_pdf}{saves all plots to single PDF file (default = FALSE).  `file_type`` must be .pdf.}
 
+\item{output_width}{the width (in inches) for output page size.  Default is NULL.}
+
+\item{output_height}{the height (in inches) for output page size.  Default is NULL.}
+
 \item{dpi}{dpi for image saving.}
 
 \item{reduction}{Dimensionality Reduction to use (if NULL then defaults to Object default)}
diff --git a/man/Iterate_Plot_Density_Joint.Rd b/man/Iterate_Plot_Density_Joint.Rd
index 8abc11079..ec31bc63b 100644
--- a/man/Iterate_Plot_Density_Joint.Rd
+++ b/man/Iterate_Plot_Density_Joint.Rd
@@ -14,6 +14,8 @@ Iterate_Plot_Density_Joint(
   file_name = NULL,
   file_type = NULL,
   single_pdf = FALSE,
+  output_width = NULL,
+  output_height = NULL,
   dpi = 600,
   reduction = NULL,
   combine = TRUE,
@@ -43,6 +45,10 @@ into file name if \code{FALSE}.}
 
 \item{single_pdf}{saves all plots to single PDF file (default = FALSE).  `file_type`` must be .pdf.}
 
+\item{output_width}{the width (in inches) for output page size.  Default is NULL.}
+
+\item{output_height}{the height (in inches) for output page size.  Default is NULL.}
+
 \item{dpi}{dpi for image saving.}
 
 \item{reduction}{Dimensionality Reduction to use (if NULL then defaults to Object default)}
diff --git a/man/Iterate_VlnPlot_scCustom.Rd b/man/Iterate_VlnPlot_scCustom.Rd
index 45d517463..e62cd6fdd 100644
--- a/man/Iterate_VlnPlot_scCustom.Rd
+++ b/man/Iterate_VlnPlot_scCustom.Rd
@@ -15,6 +15,8 @@ Iterate_VlnPlot_scCustom(
   file_name = NULL,
   file_type = NULL,
   single_pdf = FALSE,
+  output_width = NULL,
+  output_height = NULL,
   raster = NULL,
   dpi = 600,
   ggplot_default_colors = FALSE,
@@ -46,6 +48,10 @@ default is the current active.ident of the object.}
 
 \item{single_pdf}{saves all plots to single PDF file (default = FALSE).  `file_type`` must be .pdf.}
 
+\item{output_width}{the width (in inches) for output page size.  Default is NULL.}
+
+\item{output_height}{the height (in inches) for output page size.  Default is NULL.}
+
 \item{raster}{Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 100,000 total points plotted (# Cells x # of features).}
 

From 723af62b92c11fa06117659e777a95e9d17299dd Mon Sep 17 00:00:00 2001
From: samuel-marsh <samuel.marsh@childrens.harvard.edu>
Date: Thu, 12 Dec 2024 09:01:38 -0500
Subject: [PATCH 19/26] Update changelog

---
 NEWS.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index f8d77a9a3..e6185bca5 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,6 @@
 # scCustomize 3.0.1 (2024-12-11)  
 ## Added  
+- Added new parameters `output_width` and `output_height` to the `Iterate_*` family of plotting functions ([#217](https://github.com/samuel-marsh/scCustomize/issues/217)).  
   
   
 ## Changed  
@@ -9,6 +10,7 @@
 - Fixed bug in `Random_Cells_Downsample` that prevented setting identity using the `group.by` parameter.  
 - Fixed bug in `Cell_Highlight_Plot` that didn't pass the reduction parameter properly ([#216](https://github.com/samuel-marsh/scCustomize/issues/216)).  
 - Fixed bug when retrieving ensembl IDs for IEGs.  
+- Fixed bug that prevented using `return_plots` in iterative plotting functions([#217](https://github.com/samuel-marsh/scCustomize/issues/217)).  
 
 
 

From c61e50b16a15849f967fe13845a79ef507505751 Mon Sep 17 00:00:00 2001
From: samuel-marsh <samuel.marsh@childrens.harvard.edu>
Date: Thu, 12 Dec 2024 09:01:47 -0500
Subject: [PATCH 20/26] bump date

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 8c0a16ec9..39b6d5c40 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -3,7 +3,7 @@ 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> RRID:SCR_024675.
 Version: 3.0.1
-Date: 2024-12-11
+Date: 2024-12-12
 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"),

From 99fc9a286e8a6ee43a0193003b293c04b65b24e8 Mon Sep 17 00:00:00 2001
From: samuel-marsh <samuel.marsh@childrens.harvard.edu>
Date: Thu, 12 Dec 2024 09:38:03 -0500
Subject: [PATCH 21/26] add numeric checks for output height/width

---
 R/Plotting_Seurat_Iterative.R | 91 +++++++++++++++++++++++++++++++++++
 1 file changed, 91 insertions(+)

diff --git a/R/Plotting_Seurat_Iterative.R b/R/Plotting_Seurat_Iterative.R
index 06c336129..accd5391c 100644
--- a/R/Plotting_Seurat_Iterative.R
+++ b/R/Plotting_Seurat_Iterative.R
@@ -163,6 +163,19 @@ Iterate_DimPlot_bySample <- function(
   # Check Seurat
   Is_Seurat(seurat_object = seurat_object)
 
+  # check non-default output values
+  if (!is.null(x = output_width)) {
+    if (!is.numeric(x = output_width)) {
+      cli_abort(message = "The value provided to {.code output_width} ({.field {output_width}}) is is not numeric.")
+    }
+  }
+
+  if (!is.null(x = output_height)) {
+    if (!is.numeric(x = output_height)) {
+      cli_abort(message = "The value provided to {.code output_height} ({.field {output_height}}) is is not numeric.")
+    }
+  }
+
   # Harmonize pt.size across all plots
   pt.size <- pt.size %||% AutoPointSize_scCustom(data = seurat_object)
 
@@ -398,6 +411,19 @@ Iterate_Cluster_Highlight_Plot <- function(
   # Check Seurat
   Is_Seurat(seurat_object = seurat_object)
 
+  # check non-default output values
+  if (!is.null(x = output_width)) {
+    if (!is.numeric(x = output_width)) {
+      cli_abort(message = "The value provided to {.code output_width} ({.field {output_width}}) is is not numeric.")
+    }
+  }
+
+  if (!is.null(x = output_height)) {
+    if (!is.numeric(x = output_height)) {
+      cli_abort(message = "The value provided to {.code output_height} ({.field {output_height}}) is is not numeric.")
+    }
+  }
+
   # Set file_path before path check if current dir specified as opposed to leaving set to NULL
   if (!is.null(x = file_path) && file_path == "") {
     file_path <- NULL
@@ -602,6 +628,19 @@ Iterate_Meta_Highlight_Plot <- function(
   # Check Seurat
   Is_Seurat(seurat_object = seurat_object)
 
+  # check non-default output values
+  if (!is.null(x = output_width)) {
+    if (!is.numeric(x = output_width)) {
+      cli_abort(message = "The value provided to {.code output_width} ({.field {output_width}}) is is not numeric.")
+    }
+  }
+
+  if (!is.null(x = output_height)) {
+    if (!is.numeric(x = output_height)) {
+      cli_abort(message = "The value provided to {.code output_height} ({.field {output_height}}) is is not numeric.")
+    }
+  }
+
   # Check meta data
   meta_data_column <- Meta_Present(object = seurat_object, meta_col_names = meta_data_column, omit_warn = FALSE, print_msg = FALSE)[[1]]
 
@@ -922,6 +961,19 @@ Iterate_FeaturePlot_scCustom <- function(
   # Check Seurat
   Is_Seurat(seurat_object = seurat_object)
 
+  # check non-default output values
+  if (!is.null(x = output_width)) {
+    if (!is.numeric(x = output_width)) {
+      cli_abort(message = "The value provided to {.code output_width} ({.field {output_width}}) is is not numeric.")
+    }
+  }
+
+  if (!is.null(x = output_height)) {
+    if (!is.numeric(x = output_height)) {
+      cli_abort(message = "The value provided to {.code output_height} ({.field {output_height}}) is is not numeric.")
+    }
+  }
+
   # Add raster check for scCustomize
   raster <- raster %||% (length(x = Cells(x = seurat_object)) > 2e5)
 
@@ -1256,6 +1308,19 @@ Iterate_VlnPlot_scCustom <- function(
   # Check Seurat
   Is_Seurat(seurat_object = seurat_object)
 
+  # check non-default output values
+  if (!is.null(x = output_width)) {
+    if (!is.numeric(x = output_width)) {
+      cli_abort(message = "The value provided to {.code output_width} ({.field {output_width}}) is is not numeric.")
+    }
+  }
+
+  if (!is.null(x = output_height)) {
+    if (!is.numeric(x = output_height)) {
+      cli_abort(message = "The value provided to {.code output_height} ({.field {output_height}}) is is not numeric.")
+    }
+  }
+
   # Add pt.size check
   pt.size <- pt.size %||% AutoPointSize_scCustom(data = seurat_object)
 
@@ -1452,6 +1517,19 @@ Iterate_Plot_Density_Custom <- function(
   # Check Seurat
   Is_Seurat(seurat_object = seurat_object)
 
+  # check non-default output values
+  if (!is.null(x = output_width)) {
+    if (!is.numeric(x = output_width)) {
+      cli_abort(message = "The value provided to {.code output_width} ({.field {output_width}}) is is not numeric.")
+    }
+  }
+
+  if (!is.null(x = output_height)) {
+    if (!is.numeric(x = output_height)) {
+      cli_abort(message = "The value provided to {.code output_height} ({.field {output_height}}) is is not numeric.")
+    }
+  }
+
   # joint check
   if (!is.null(x = joint)) {
     cli_abort(message = c("{.code Iterate_Plot_Density_Custom} only supports {.code joint = FALSE}.",
@@ -1657,6 +1735,19 @@ Iterate_Plot_Density_Joint <- function(
   # Check Seurat
   Is_Seurat(seurat_object = seurat_object)
 
+  # check non-default output values
+  if (!is.null(x = output_width)) {
+    if (!is.numeric(x = output_width)) {
+      cli_abort(message = "The value provided to {.code output_width} ({.field {output_width}}) is is not numeric.")
+    }
+  }
+
+  if (!is.null(x = output_height)) {
+    if (!is.numeric(x = output_height)) {
+      cli_abort(message = "The value provided to {.code output_height} ({.field {output_height}}) is is not numeric.")
+    }
+  }
+
   # Check gene list is in list form
   if (!inherits(x = gene_list, what = "list")) {
     cli_abort(message = c("For {.code Iterate_Plot_Density_Joint} the {.code gene_list} must be of class(): {.val list}",

From baea6369f0f8f10704b81dce5c3a8d46837e4064 Mon Sep 17 00:00:00 2001
From: samuel-marsh <samuel.marsh@childrens.harvard.edu>
Date: Thu, 12 Dec 2024 09:41:40 -0500
Subject: [PATCH 22/26] fix typo

---
 R/Plotting_Seurat_Iterative.R | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/R/Plotting_Seurat_Iterative.R b/R/Plotting_Seurat_Iterative.R
index accd5391c..e5c94b6bd 100644
--- a/R/Plotting_Seurat_Iterative.R
+++ b/R/Plotting_Seurat_Iterative.R
@@ -166,13 +166,13 @@ Iterate_DimPlot_bySample <- function(
   # check non-default output values
   if (!is.null(x = output_width)) {
     if (!is.numeric(x = output_width)) {
-      cli_abort(message = "The value provided to {.code output_width} ({.field {output_width}}) is is not numeric.")
+      cli_abort(message = "The value provided to {.code output_width} ({.field {output_width}}) is not numeric.")
     }
   }
 
   if (!is.null(x = output_height)) {
     if (!is.numeric(x = output_height)) {
-      cli_abort(message = "The value provided to {.code output_height} ({.field {output_height}}) is is not numeric.")
+      cli_abort(message = "The value provided to {.code output_height} ({.field {output_height}}) is not numeric.")
     }
   }
 
@@ -414,13 +414,13 @@ Iterate_Cluster_Highlight_Plot <- function(
   # check non-default output values
   if (!is.null(x = output_width)) {
     if (!is.numeric(x = output_width)) {
-      cli_abort(message = "The value provided to {.code output_width} ({.field {output_width}}) is is not numeric.")
+      cli_abort(message = "The value provided to {.code output_width} ({.field {output_width}}) is not numeric.")
     }
   }
 
   if (!is.null(x = output_height)) {
     if (!is.numeric(x = output_height)) {
-      cli_abort(message = "The value provided to {.code output_height} ({.field {output_height}}) is is not numeric.")
+      cli_abort(message = "The value provided to {.code output_height} ({.field {output_height}}) is not numeric.")
     }
   }
 
@@ -631,13 +631,13 @@ Iterate_Meta_Highlight_Plot <- function(
   # check non-default output values
   if (!is.null(x = output_width)) {
     if (!is.numeric(x = output_width)) {
-      cli_abort(message = "The value provided to {.code output_width} ({.field {output_width}}) is is not numeric.")
+      cli_abort(message = "The value provided to {.code output_width} ({.field {output_width}}) is not numeric.")
     }
   }
 
   if (!is.null(x = output_height)) {
     if (!is.numeric(x = output_height)) {
-      cli_abort(message = "The value provided to {.code output_height} ({.field {output_height}}) is is not numeric.")
+      cli_abort(message = "The value provided to {.code output_height} ({.field {output_height}}) is not numeric.")
     }
   }
 
@@ -964,13 +964,13 @@ Iterate_FeaturePlot_scCustom <- function(
   # check non-default output values
   if (!is.null(x = output_width)) {
     if (!is.numeric(x = output_width)) {
-      cli_abort(message = "The value provided to {.code output_width} ({.field {output_width}}) is is not numeric.")
+      cli_abort(message = "The value provided to {.code output_width} ({.field {output_width}}) is not numeric.")
     }
   }
 
   if (!is.null(x = output_height)) {
     if (!is.numeric(x = output_height)) {
-      cli_abort(message = "The value provided to {.code output_height} ({.field {output_height}}) is is not numeric.")
+      cli_abort(message = "The value provided to {.code output_height} ({.field {output_height}}) is not numeric.")
     }
   }
 
@@ -1311,13 +1311,13 @@ Iterate_VlnPlot_scCustom <- function(
   # check non-default output values
   if (!is.null(x = output_width)) {
     if (!is.numeric(x = output_width)) {
-      cli_abort(message = "The value provided to {.code output_width} ({.field {output_width}}) is is not numeric.")
+      cli_abort(message = "The value provided to {.code output_width} ({.field {output_width}}) is not numeric.")
     }
   }
 
   if (!is.null(x = output_height)) {
     if (!is.numeric(x = output_height)) {
-      cli_abort(message = "The value provided to {.code output_height} ({.field {output_height}}) is is not numeric.")
+      cli_abort(message = "The value provided to {.code output_height} ({.field {output_height}}) is not numeric.")
     }
   }
 
@@ -1520,13 +1520,13 @@ Iterate_Plot_Density_Custom <- function(
   # check non-default output values
   if (!is.null(x = output_width)) {
     if (!is.numeric(x = output_width)) {
-      cli_abort(message = "The value provided to {.code output_width} ({.field {output_width}}) is is not numeric.")
+      cli_abort(message = "The value provided to {.code output_width} ({.field {output_width}}) is not numeric.")
     }
   }
 
   if (!is.null(x = output_height)) {
     if (!is.numeric(x = output_height)) {
-      cli_abort(message = "The value provided to {.code output_height} ({.field {output_height}}) is is not numeric.")
+      cli_abort(message = "The value provided to {.code output_height} ({.field {output_height}}) is not numeric.")
     }
   }
 
@@ -1738,13 +1738,13 @@ Iterate_Plot_Density_Joint <- function(
   # check non-default output values
   if (!is.null(x = output_width)) {
     if (!is.numeric(x = output_width)) {
-      cli_abort(message = "The value provided to {.code output_width} ({.field {output_width}}) is is not numeric.")
+      cli_abort(message = "The value provided to {.code output_width} ({.field {output_width}}) is not numeric.")
     }
   }
 
   if (!is.null(x = output_height)) {
     if (!is.numeric(x = output_height)) {
-      cli_abort(message = "The value provided to {.code output_height} ({.field {output_height}}) is is not numeric.")
+      cli_abort(message = "The value provided to {.code output_height} ({.field {output_height}}) is not numeric.")
     }
   }
 

From 154aaa1ad21f6732b9503921aa70ab9822bd2bb9 Mon Sep 17 00:00:00 2001
From: samuel-marsh <samuel.marsh@childrens.harvard.edu>
Date: Wed, 18 Dec 2024 09:17:29 -0500
Subject: [PATCH 23/26] update r proj

---
 scCustomize.Rproj | 1 +
 1 file changed, 1 insertion(+)

diff --git a/scCustomize.Rproj b/scCustomize.Rproj
index d0ded0715..d65c29a9a 100644
--- a/scCustomize.Rproj
+++ b/scCustomize.Rproj
@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 36c01bc4-551d-46b8-b881-69c09777ce3d
 
 RestoreWorkspace: Default
 SaveWorkspace: Default

From 591c06a72149524190ea494befd68dc5176cd87b Mon Sep 17 00:00:00 2001
From: samuel-marsh <samuel.marsh@childrens.harvard.edu>
Date: Wed, 18 Dec 2024 09:18:06 -0500
Subject: [PATCH 24/26] update changelog

---
 NEWS.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index e6185bca5..28a354222 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# scCustomize 3.0.1 (2024-12-11)  
+# scCustomize 3.0.1 (2024-12-18)  
 ## Added  
 - Added new parameters `output_width` and `output_height` to the `Iterate_*` family of plotting functions ([#217](https://github.com/samuel-marsh/scCustomize/issues/217)).  
   

From 35310192b2d1cf45a606dbe68178e8545eeabb17 Mon Sep 17 00:00:00 2001
From: samuel-marsh <samuel.marsh@childrens.harvard.edu>
Date: Wed, 18 Dec 2024 09:18:13 -0500
Subject: [PATCH 25/26] bump version

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 39b6d5c40..cd09ae999 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -3,7 +3,7 @@ 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> RRID:SCR_024675.
 Version: 3.0.1
-Date: 2024-12-12
+Date: 2024-12-18
 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"),

From 56e5fca4a67c56977dc8e02618af1461aab40b61 Mon Sep 17 00:00:00 2001
From: samuel-marsh <samuel.marsh@childrens.harvard.edu>
Date: Wed, 18 Dec 2024 09:18:58 -0500
Subject: [PATCH 26/26] Update cran comments

---
 cran-comments.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cran-comments.md b/cran-comments.md
index 81a17352d..93a2849a6 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,5 +1,5 @@
 ## Hotfix Update 
-This is major update to version 3.0.1.  Fixes bug preventing a function from operating correctly.  See News.md for full changelog.  
+This is major update to version 3.0.1.  Fixes 4 minor bugs that caused unexpected errors.  See News.md for full changelog.