plotMolecules {ggspavis}R Documentation

plotMolecules

Description

Plotting functions for spatially resolved transcriptomics data.

Usage

plotMolecules(
  spe,
  molecule = NULL,
  x_coord = "x",
  y_coord = "y",
  palette = c("gray90", "navy"),
  size = 0.3
)

Arguments

spe

(SpatialExperiment) Input data, assumed to be a SpatialExperiment object.

molecule

(character) Name of mRNA molecule to plot (assumed to match one of the row names of rowData).

x_coord

(character) Name of column in spatialCoords containing x-coordinates of the cell centroids. Default = "x".

y_coord

(character) Name of column in spatialCoords containing y-coordinates of the cell centroids. Default = "y".

palette

(character) Color palette, provided as a vector of length 2 for the low and high range. Default = c("gray90", "navy").

size

(numeric) Point size for geom_point(). Default = 0.3.

Details

Function to plot molecule-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), for a selected molecule.

Value

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

Examples

library(STexampleData)
spe <- seqFISH_mouseEmbryo()
plotMolecules(spe, molecule = "Sox2")


[Package ggspavis version 1.0.0 Index]