Adding more space around the plots

AlicenJoyHenning · Sep 12, 2024 · 875e900 · 875e900
1 parent edb1fb4
commit 875e900
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Showing 3 changed files with 14 additions and 14 deletions.
diff --git a/R/create_imc_plot.R b/R/create_imc_plot.R
@@ -17,7 +17,7 @@
 #' @export
 #'
 #' @keywords internal
-#' 
+#'
 #' @examples
 #' \dontrun{
 #' # Example usage:
@@ -48,8 +48,8 @@ create_imc_plot <- function(imc_df, project_name, IMC_percent) {
     ) +
     theme_classic() +
     theme(
-      plot.margin = unit(c(0.2, 0.2, 0.2, 0.4), 'cm'),
       plot.title = element_text(hjust = 0.5, face = "bold", size = 12),
+      plot.margin = unit(c(1, 1, 1, 1), 'cm'),
       axis.title.x = element_text(hjust = 0.5, vjust = -1, face = "bold", size = 12),
       axis.title.y = element_text(hjust = 0.5, vjust = 3, face = "bold", size = 12),
       axis.text.x = element_text(angle = 0, hjust = 0.5, vjust = -1.2, size = 12),

diff --git a/R/create_rbc_plot.R b/R/create_rbc_plot.R
@@ -18,7 +18,7 @@
 #' @export
 #'
 #' @keywords internal
-#' 
+#'
 #' @examples
 #' \dontrun{
 #' # Assuming `rbc_data` is a data frame containing the RBC data.
@@ -30,7 +30,7 @@
 #' project_name <- "RBC Contamination Analysis"
 #' RBC_percent <- 15.0
 #' initial_cells <- 1000
-#' 
+#'
 #' plot <- create_rbc_plot(rbc_data, project_name, RBC_percent, initial_cells)
 #' print(plot)
 #' }
@@ -61,8 +61,8 @@ create_rbc_plot <- function(rbc_df, project_name, RBC_percent, initial_cells) {
       legend.position = "below",
       legend.box.background = element_rect(colour = "black"),
       strip.background = element_blank(),
-      plot.margin = unit(c(0.2, 0.2, 0.2, 0.4), 'cm'),
       plot.title = element_text(hjust = 0.5, face = "bold", size = 12),
+      plot.margin = unit(c(1, 1, 1, 1), 'cm'),
       panel.background = element_blank(),
       panel.grid = element_blank(),
       panel.border = element_rect(colour = "black", fill = NA, linewidth = 1)

diff --git a/R/limiric_core.R b/R/limiric_core.R
@@ -82,7 +82,7 @@ limiric_core <- function(
 ){
   # Receive & prepare input ------------------------------------
 
-  message("\nBeginning  limiric  analysis for", project_name, "...\n")
+  message("\nBeginning limiric analysis for ", project_name, "...\n")
 
   # Ensure calculations are reproducible
   set.seed(7777)
@@ -356,7 +356,7 @@ limiric_core <- function(
   limiric <- limiric_output$limiric
 
 
-  message("\u2714 limiric  damaged cell predictions\n")
+  message("\u2714 limiric damaged cell predictions\n")
 
 
 
@@ -441,7 +441,7 @@ limiric_core <- function(
     annotated_cells <- merge(storage_cells, clean_cells, by = "barcode", all.x = TRUE)
     annotated_cells$QC_annotation[is.na(annotated_cells$QC_annotation)] <- "removed"
 
-    write.csv(annotated_cells, file = file.path(output_path, "DropletQC", paste0(project_name, "_barcodes.csv")), row.names = FALSE)
+    write.csv(annotated_cells, file = file.path(output_path, "DropletQC", paste0(project_name, "_barcodes.csv")), row.names = FALSE, quote = FALSE)
 
     # Rename column
     Seurat$limiric.droplet_qc <- Seurat$QC
@@ -459,7 +459,7 @@ limiric_core <- function(
 
     # Save a list of barcodes with limiric annotations (cell, damaged)
     clean_cells <- data.frame(barcode = rownames(Seurat@meta.data), limiric = Seurat@meta.data$limiric)
-    write.csv(clean_cells, file = file.path(output_path, "Filtered", paste0(project_name, "_barcodes.csv")), row.names = FALSE)
+    write.csv(clean_cells, file = file.path(output_path, "Filtered", paste0(project_name, "_barcodes.csv")), row.names = FALSE, quote = FALSE)
 
     Seurat <- subset(Seurat, QC != "agreed")
 
@@ -482,13 +482,13 @@ limiric_core <- function(
     # Save a list of barcodes with limiric annotations (cell, damaged)
     storage_cells <- data.frame(barcode = rownames(storage@meta.data))
     clean_cells <- data.frame(barcode = rownames(Seurat@meta.data), limiric = Seurat@meta.data$limiric)
-    write.csv(clean_cells, file = file.path(output_path, "/Filtered/", paste0(project_name, "_barcodes.csv")), row.names = FALSE)
+    write.csv(clean_cells, file = file.path(output_path, "/Filtered/", paste0(project_name, "_barcodes.csv")), row.names = FALSE, quote = FALSE)
 
     # Account for cells that may have been filtered
     annotated_cells <- merge(storage_cells, clean_cells, by = "barcode", all.x = TRUE)
     annotated_cells$limiric[is.na(annotated_cells$limiric)] <- "removed"
 
-    write.csv(annotated_cells, file = file.path(output_path, "Filtered", paste0(project_name, "_barcodes.csv")), row.names = FALSE)
+    write.csv(annotated_cells, file = file.path(output_path, "Filtered", paste0(project_name, "_barcodes.csv")), row.names = FALSE, quote = FALSE)
 
 
     # Filter damaged cells only according to limiric estimations
@@ -515,18 +515,18 @@ limiric_core <- function(
     # Save a list of barcodes with limiric annotations (cell, damaged)
     storage_cells <- data.frame(barcode = rownames(storage@meta.data))
     clean_cells <- data.frame(barcode = rownames(Seurat@meta.data), limiric = Seurat@meta.data$limiric)
-    write.csv(clean_cells, file = file.path(output_path, "/Filtered/", paste0(project_name, "_barcodes.csv")), row.names = FALSE)
+    write.csv(clean_cells, file = file.path(output_path, "/Filtered/", paste0(project_name, "_barcodes.csv")), row.names = FALSE, quote = FALSE)
 
     # Account for cells that may have been filtered
     annotated_cells <- merge(storage_cells, clean_cells, by = "barcode", all.x = TRUE)
     annotated_cells$limiric[is.na(annotated_cells$limiric)] <- "removed"
 
-    write.csv(annotated_cells, file = file.path(output_path, "Filtered", paste0(project_name, "_barcodes.csv")), row.names = FALSE)
+    write.csv(annotated_cells, file = file.path(output_path, "Filtered", paste0(project_name, "_barcodes.csv")), row.names = FALSE, quote = FALSE)
     saveRDS(Seurat, file.path(output_path, "Filtered", paste0(project_name, "_unfiltered.rds")))
 
   }
 
-  message("\u2714 limiric  analysis complete.\n\n")
+  message("\u2714 limiric analysis complete\n\n")
 
   return(Seurat)