Minor fix for codes to pass Check

.gitignore

@@ -3,4 +3,4 @@
 *.png
 Rcheck.txt
 .Rproj.user
-NAMESPACE
+*.txt

DESCRIPTION

@@ -61,6 +61,11 @@ Imports:
     png,
     httr,
     jsonlite,
-    plyr
+    plyr,
+    colorspace,
+    dendextend,
+    dendsort,
+    pheatmap,
+    scales
 Config/testthat/edition: 3
 

NAMESPACE

@@ -0,0 +1,73 @@
+# Generated by roxygen2: do not edit by hand
+
+export(DotplotMet)
+export(DualLabeling)
+export(Filter_and_QC)
+export(Heatmap)
+export(MetadataTable)
+export(ModuleScore)
+export(NameClusters)
+export(Pseudobulk_DEG)
+export(SampleNames)
+export(ViolinPlot)
+export(color_by_genes)
+export(harmony_batch_correct)
+export(palantir_api_call)
+export(tSNE3D)
+export(tSNE_3D_Coordinates)
+import(RColorBrewer)
+import(Seurat)
+import(colorspace)
+import(cowplot)
+import(data.table)
+import(dendextend)
+import(dendsort)
+import(dplyr)
+import(edgeR)
+import(ggplot2)
+import(ggpubr)
+import(grid)
+import(gridExtra)
+import(harmony)
+import(httr)
+import(jsonlite)
+import(limma)
+import(magrittr)
+import(pheatmap)
+import(plyr)
+import(png)
+import(purrr)
+import(quantmod)
+import(reshape2)
+import(rlang)
+import(statmod)
+import(stringr)
+import(svglite)
+import(tidyverse)
+import(utils)
+importFrom(Seurat,AddMetaData)
+importFrom(dplyr,arrange)
+importFrom(dplyr,case_when)
+importFrom(dplyr,mutate)
+importFrom(dplyr,pull)
+importFrom(dplyr,select)
+importFrom(ggplot2,aes)
+importFrom(ggplot2,geom_point)
+importFrom(ggplot2,ggplot)
+importFrom(ggplot2,ggtitle)
+importFrom(ggplot2,scale_y_reverse)
+importFrom(ggplot2,theme)
+importFrom(ggplot2,theme_classic)
+importFrom(ggplot2,ylim)
+importFrom(grid,grid.draw)
+importFrom(gridExtra,arrangeGrob)
+importFrom(methods,slotNames)
+importFrom(plotly,as_widget)
+importFrom(plotly,ggplotly)
+importFrom(plotly,plot_ly)
+importFrom(reshape2,melt)
+importFrom(scales,rescale)
+importFrom(stats,quantile)
+importFrom(tibble,deframe)
+importFrom(tibble,rownames_to_column)
+importFrom(tibble,tibble)

R/Dotplot_by_Metadata.R

@@ -53,7 +53,7 @@ DotplotMet <- function(object,
           labs(y=metadata)
 
   # Generate Contingency Table for Annotated cell types
-  sample_column = sub("_",".",sample_column)
+  sample_column = sub("_",".",sample.column)
   cluster_num <- as.data.frame.matrix(table(object@meta.data[[sample_column]],object@meta.data[[metadata]]))
   cluster_num %>% rownames_to_column("Samples") -> cluster_num
 

R/Dual_Labeling.R

@@ -71,17 +71,17 @@ DualLabeling <- function(object,
   ##--------------- ##
   ## Error Messages ##
   ## -------------- ##
-  
-  if(!(marker1 %in% rownames(obj))){
+
+  if(!(marker1 %in% rownames(object))){
     stop(paste0("ERROR: ",marker1," is not found in dataset"))
   }
-  if(!(marker2 %in% rownames(obj))){
+  if(!(marker2 %in% rownames(object))){
     stop(paste0("ERROR: ",marker2," is not found in dataset"))
   }
-  if(!(marker_1_type %in% names(obj@assays))){
+  if(!(marker_1_type %in% names(object@assays))){
     stop(paste0("ERROR: ",marker_1_type," slot is not found in dataset"))
   }
-  if(!(marker_2_type %in% names(obj@assays))){
+  if(!(marker_2_type %in% names(object@assays))){
     stop(paste0("ERROR: ",marker_2_type," slot is not found in dataset"))
   }