plotSpots {ggspavis} | R Documentation

## plotSpots

### Description

Plotting functions for spatially resolved transcriptomics data.

### Usage

    plotSpots(
      spe,
      x_coord = "x",
      y_coord = "y",
      in_tissue = "in_tissue",
      annotate = NULL,
      palette = "libd_layer_colors",
      y_reverse = TRUE,
      size = 0.3
    )

### Arguments

`spe` | (SpatialExperiment) Input data, assumed to be a `SpatialExperiment` object.
`x_coord` | (character) Name of column in `spatialCoords` containing x-coordinates. Default = "x".
`y_coord` | (character) Name of column in `spatialCoords` containing y-coordinates. Default = "y".
`in_tissue` | (character) Name of column in `spatialData` identifying spots over tissue, e.g. "in_tissue" for 10x Genomics Visium data. If this argument is provided, only spots over tissue will be shown. Alternatively, set to NULL to display all spots. Default = "in_tissue".
`annotate` | (character) Name of column in `colData` containing values to annotate spots with colors, e.g. cluster labels (discrete values) or total UMI counts (continuous values). For discrete values such as cluster labels, the column in `colData` should be formatted as a factor.
`palette` | (character) Color palette for annotation. Options for discrete labels (e.g. cluster labels) are "libd_layer_colors", "Okabe-Ito", or a vector of color names or hex values. For continuous values (e.g. total UMI counts), provide a vector of length 2 for the low and high range, e.g. `c("gray90", "navy")`. Default = `"libd_layer_colors"`.
`y_reverse` | (logical) Whether to reverse y coordinates, which is often required for 10x Genomics Visium data. Default = TRUE.
`size` | (numeric) Point size for `geom_point()`. Default = 0.3.

### Details

Function to plot spot-based spatially resolved transcriptomics data stored in a `SpatialExperiment` object.

This function generates a plot in spatial coordinates (e.g. x-y coordinates on a tissue slide), along with annotation such as cluster labels or total UMI counts.

### Value

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

### Examples

    library(STexampleData)
    spe <- Visium_humanDLPFC()
    plotSpots(spe, annotate = "ground_truth")

[Package ggspavis version 1.0.0 Index]