plotVisium {ggspavis} | R Documentation

## plotVisium

### Description

Plots for spatially resolved transcriptomics data from the 10x Genomics Visium platform

### Usage

    plotVisium(
      spe,
      spots = TRUE,
      fill = NULL,
      highlight = NULL,
      facets = "sample_id",
      image = TRUE,
      assay = "logcounts",
      trans = "identity",
      x_coord = "x",
      y_coord = "y",
      y_reverse = TRUE,
      sample_ids = NULL,
      image_ids = NULL,
      palette = NULL
    )

### Arguments

`spe` | (SpatialExperiment) Input data object.
`spots` | (logical) Whether to display spots (spatial barcodes) as points. Default = TRUE.
`fill` | (character) Column in `colData` to use to fill points by color. If `fill` contains a numeric column (e.g. total UMI counts), a continuous color scale will be used. If `fill` contains a factor (e.g. cluster labels), a discrete color scale will be used. Default = NULL.
`highlight` | (character) Column in `spatialData` to use to highlight points by outlining them. For example, `in_tissue` will highlight spots overlapping with tissue. Default = NULL.
`facets` | (character) Column in `colData` to use to facet plots, i.e. show multiple panels of plots. Default = "sample_id". Set to NULL to disable.
`image` | (logical) Whether to show histology image as background. Default = TRUE.
`assay` | (character) Name of assay data to use when `fill` is in `rownames(spe)`. Should be one of `assayNames(spe)`.
`trans` | Transformation to apply for continuous scales. Ignored unless `fill` is numeric, e.g. feature expression. (See `ggplot2{continuous_scale}` for valid options.)
`x_coord` | (character) Column in `spatialCoords` containing x-coordinates. Default = "x".
`y_coord` | (character) Column in `spatialCoords` containing y-coordinates. Default = "y".
`y_reverse` | (logical) Whether to reverse y coordinates, which is often required for Visium data, depending on the orientation of the raw data. Default = TRUE.
`sample_ids` | (character) Samples to show, if multiple samples are available. Default = NULL (show all samples).
`image_ids` | (character) Images to show, if multiple images are available. Default = NULL (show all images).
`palette` | (character) Color palette for points. Options for discrete labels are "libd_layer_colors", "Okabe-Ito", or a custom vector of hex color codes. Options for continuous values are "viridis", a single color name (e.g. "red", "navy", etc), or a vector of length two containing color names for each end of the scale. Default = "libd_layer_colors" for discrete data, and "viridis" for continuous data.

### Details

Function to generate plots for spatially resolved transcriptomics datasets from the 10x Genomics Visium spatially platform.

This function generates a plot for spot-based spatially resolved transcriptomics data from the 10x Genomics Visium platform, with several options available to adjust the plot type and style.

### Value

Returns a ggplot object. Additional plot elements can be added as ggplot elements (e.g. title, customized formatting, etc).

### Author(s)

Helena L. Crowell with modifications by Lukas M. Weber

### Examples

    library(STexampleData)

    spe <- Visium_mouseCoronal()

    # color by x coordinate, highlight in-tissue spots
    plotVisium(spe, fill = "x", highlight = "in_tissue")

    # subset in-tissue spots
    sub <- spe[, as.logical(spatialData(spe)$in_tissue)]

    # color by feature counts, don't include image
    rownames(sub) <- make.names(rowData(sub)$gene_name)
    plotVisium(sub, fill = "Gad2", assay = "counts")

[Package ggspavis version 1.0.0 Index]