plotMolecules {ggspavis} | R Documentation |
Plotting functions for spatially resolved transcriptomics data.
plotMolecules( spe, molecule = NULL, x_coord = "x", y_coord = "y", palette = c("gray90", "navy"), size = 0.3 )
spe |
(SpatialExperiment) Input data, assumed to be a
|
molecule |
(character) Name of mRNA molecule to plot (assumed to match
one of the row names of |
x_coord |
(character) Name of column in |
y_coord |
(character) Name of column in |
palette |
(character) Color palette, provided as a vector of length 2
for the low and high range. Default = |
size |
(numeric) Point size for |
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.
Returns a ggplot object. Additional plot elements can be added as ggplot elements (e.g. title, labels, formatting, etc).
library(STexampleData) spe <- seqFISH_mouseEmbryo() plotMolecules(spe, molecule = "Sox2")