spanielPlot: Spatial Transcriptomics Plot

In Spaniel: Spatial Transcriptomics Analysis

Description

This function overlays information from a Seurat object or SingleCellExperiment object containing barcodes onto a H & E image. There are 4 plots available showing a) the number of genes detected per spot, b) the number of reads detected per spot, c) clustering results, d) the gene expression of a selected gene.

Usage

spanielPlot(object, grob, plotType = c("NoGenes",
                                            "CountsPerSpot",
                                            "Cluster",
                                            "Gene"),
                gene= NULL, clusterRes = NULL, customTitle = NULL,
                scaleData = TRUE, showFilter = NULL, ptSize = 2,
                ptSizeMin = 0, ptSizeMax = 5)

Arguments

object	Either a Seurat object (version 3) or a SingleCellExperiment object containing barcode coordinates in the metadata (Seurat) or colData (SingleCellExperiment).
grob	an grob to be used as the backgound image see(parseImage)
plotType	There are 5 types of plots avaiable: 1) NoGenes - This shows the number of genes per spot and uses information from "nFeature_RNA" column of Seurat object or "detected" from a SingleCellExperiment object. 2) CountsPerSpot - This shows the number of counts per spot. It uses information from "nCount_RNA" column of Seurat object or "sum" from a singleCellExperiment object. 3) Cluster - This plot is designed to show clustering results stored in the meta.data or colData of an object 4) Gene- This plot shows the expression of a single gene. This plot uses scaled/normalised expressin data from the scale.data slot of Seurat object or logcounts of a SingleCellExperiment object. 5) Other - A generic plot to plot any column from the meta.data or colData of an object.
gene	Gene to plot
clusterRes	which cluster resolution to plot
customTitle	Specify plot title (optional)
scaleData	Show scaled data on plot (default is TRUE)
showFilter	Logical filter showing pass/fail for spots
ptSize	Point size used for cluster plot default is 2
ptSizeMin	Minimum point size used for QC and Gene Expression plots default is 0
ptSizeMax	Maximum point size used for QC and Gene Expression plots default is 5

Value

A ggplot spatial transcriptomics plot

Examples

## Data is taken from DOI: 10.1126/science.aaf2403
SeuratObj <- readRDS(file.path(system.file(package = "Spaniel"),
                        "extdata/SeuratData.rds"))
imgFile <- readRDS(file.path(system.file(package = "Spaniel"),
                        "extdata/image.rds"))

## Counts per spot with a QC filter
minGenes <- 2000
minUMI <- 300000
filter <- SeuratObj$nFeature_RNA > minGenes &
            SeuratObj$nCount_RNA > minUMI
spanielPlot(object = SeuratObj, grob = imgFile,
        plotType = "CountsPerSpot",
        showFilter = filter)

## Cluster plot
spanielPlot(object = SeuratObj, grob = imgFile,
        plotType = "Cluster",
        clusterRes = "cluster_RNA_snn_res.0.6")

## Gene plot
spanielPlot(object = SeuratObj, grob = imgFile,
        plotType = "Gene",
        gene= "Nrgn")

Spaniel documentation built on Nov. 8, 2020, 5:54 p.m.