bug fixes (d3941a28) · Commits · github_fork / Plot1cell

DESCRIPTION

+4 −2

Original line number	Diff line number	Diff line
		@@ -36,7 +36,8 @@ Imports:
		GenomeInfoDb,
		EnsDb.Hsapiens.v86,
		cowplot,
		rlang
		rlang,
		GEOquery
		Depends:
		Seurat,
		plotly,
		@@ -65,7 +66,8 @@ Depends:
		GenomeInfoDb,
		EnsDb.Hsapiens.v86,
		cowplot,
		rlang
		rlang,
		GEOquery
		License: GPL-3
		Encoding: UTF-8
		LazyData: true

NAMESPACE

+2 −0

Original line number	Diff line number	Diff line
		# Generated by roxygen2: do not edit by hand

		export(Install.example)
		export(add_sliding_windows)
		export(add_track)
		export(cell_order)
		export(change_strip_background)
		export(complex_dotplot_multiple)
		export(complex_dotplot_single)
		export(complex_featureplot)
		export(complex_vlnplot_single)
		export(convert_geneid)
		export(creat_cellphonedb_file)

R/modified_seurat_plot.R

+1 −1

Original line number	Diff line number	Diff line
		@@ -18,7 +18,7 @@ modified_dotplot <- function(
		levels(seu_obj) <- rev(levels(seu_obj))
		dataplot<-DotPlot(seu_obj, features = features)
		dataplot<-dataplot$data
		dataplot$avg.exp<-scale(dataplot$avg.exp)
		dataplot$avg.exp<-dataplot$avg.exp.scaled
		colnames(dataplot)[1:2]<-c('Avg.Exp', 'Pct.Exp')
		if(is.null(col_palette)){
		col_palette = colorRampPalette(c('grey80','lemonchiffon1','indianred1','darkred'))(255)

R/plot_circlize.R

+10 −10

Original line number	Diff line number	Diff line
		@@ -26,25 +26,25 @@ transform_coordinates <- function(
		#' This function extracts the metadata from a Seurat object and transforms the
		#' UMAP/tSNE coordinates.
		#'
		#' @param obj SeuratObject
		#' @param seu_obj SeuratObject
		#' @param reductions reductions methods, e.g."umap" or "tsne".
		#' @param color Colors assigned to the cell clusters
		#' @param coord_scale value from c(0,1) to adjust the UMAP/tSNE coordinates.
		#' @return A metadata dataframe
		#' @export
		get_metadata <- function(
		obj,
		seu_obj,
		reductions = "umap",
		coord_scale = 0.8,
		color
		){
		metadata<-obj@meta.data
		metadata$Cluster<-obj@active.ident
		metadata$dim1<-as.numeric(obj[[reductions]]@cell.embeddings[,1])
		metadata$dim2<-as.numeric(obj[[reductions]]@cell.embeddings[,2])
		metadata<-seu_obj@meta.data
		metadata$Cluster<-seu_obj@active.ident
		metadata$dim1<-as.numeric(seu_obj[[reductions]]@cell.embeddings[,1])
		metadata$dim2<-as.numeric(seu_obj[[reductions]]@cell.embeddings[,2])
		metadata$x<-transform_coordinates(metadata$dim1, zoom = coord_scale)
		metadata$y<-transform_coordinates(metadata$dim2, zoom = coord_scale)
		color_df<-data.frame(Cluster=levels(obj), Colors=color)
		color_df<-data.frame(Cluster=levels(seu_obj), Colors=color)
		cellnames<-rownames(metadata)
		metadata$cells<-rownames(metadata)
		metadata<-merge(metadata, color_df, by='Cluster')
		@@ -58,15 +58,15 @@ get_metadata <- function(
		#' This function labels the cells based their expression levels of the selected
		#' marker genes.
		#'
		#' @param obj SeuratObject
		#' @param seu_obj SeuratObject
		#' @param features Selected marker genes
		#' @return A dataframe with cells labeled by marker genes
		#' @export
		mk_marker_ct <- function(
		obj,
		seu_obj,
		features
		){
		dat <- Seurat::FetchData(obj, vars = features)
		dat <- Seurat::FetchData(seu_obj, vars = features)
		ori_names <- rownames(dat)
		zero_ct <- dat[rowSums(dat)==0,]
		non_zero <- dat[rowSums(dat)!=0,]

R/plot_dot.R

+3 −6

Original line number	Diff line number	Diff line
		@@ -4,10 +4,7 @@
		#' Plot single gene across groups
		#'
		#' This function can be used for plotting a single gene expression across
		#' different groups in a study with complex group design. It uses the data
		#' output from the DotPlot function in the Seurat package and uses ggplot2
		#' to re-create a dotplot for better visualization. In the output graph, y axis
		#' is the cluster name and x axis is the group ID.
		#' different groups in a study with complex group design.
		#'
		#' @param seu_obj A complete Seurat object
		#' @param feature Gene name. Only one gene is allowed.
		@@ -27,11 +24,11 @@ complex_dotplot_single <- function(
		do.scale=T,
		scale.by='radius'
		){
		groupby_level<-levels(seu_obj@meta.data[,groupby])
		seu_obj@meta.data[,groupby]<-gsub("_","-",seu_obj@meta.data[,groupby])
		if (is.null(levels(seu_obj@meta.data[,groupby]))){
		if (is.null(groupby_level)){
		seu_obj@meta.data[,groupby] <-factor(seu_obj@meta.data[,groupby], levels = names(table(seu_obj@meta.data[,groupby])))
		}
		groupby_level<-levels(seu_obj@meta.data[,groupby])
		levels(seu_obj)<-rev(levels(seu_obj))
		celltypes<-levels(seu_obj)
		celltypes<-gsub("_", "-", celltypes)

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