spanielPlot {Spaniel} | R Documentation

## Spatial Transcriptomics Plot

### 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 = NULL,
    techType =
    "Original",
    byCoord = FALSE,
    imgDims = NULL,
    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). This is used for original Spatial Transcriptomics objects but not Visium
`techType` | Either 1) "Original" (default) for the original Spatial Transcriptomics slides where the image has been cropped to the edge of the spots 2) "Visium" for 10X slides.
`byCoord` | TRUE/FALSE option to plot original Spatial Transcriptomics data using pixel coordinates instead of by spot coordinates. Not required if techType = "Visium". Default is FALSE.
`imgDims` | pixel dimensions of histological image. Required when byCoord parameter is set to TRUE, Not required if techType = "Visium".
`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

    pathToTenXOuts <- file.path(system.file(package = "Spaniel"), "extdata/outs")
    sceObj <- createVisiumSCE(tenXDir=pathToTenXOuts,
                           resolution="Low")
    filter <- sceObj$detected > 0
    spanielPlot(object = sceObj,
    plotType = "NoGenes",
    showFilter = filter,
    techType = "Visium",
    ptSizeMax = 3)

[Package Spaniel version 1.8.0 Index]