plot-generic: Preview a Giotto spatial object

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Preview a Giotto spatial object

Description

S4 generic for previewing Giotto's image and subcellular objects.

Usage

## S4 method for signature 'giottoImage,missing'
plot(x, y, ...)

## S4 method for signature 'giottoLargeImage,missing'
plot(x, y, ...)

## S4 method for signature 'giottoPolygon,missing'
plot(x, point_size = 0.1, type = c("poly", "centroid"), ...)

## S4 method for signature 'giottoPoints,missing'
plot(x, point_size = 0, feats = NULL, raster = TRUE, raster_size = 600, ...)

## S4 method for signature 'spatLocsObj,missing'
plot(x, y, ...)

## S4 method for signature 'spatialNetworkObj,missing'
plot(x, y, ...)

Arguments

x	giotto image, giottoPolygon, or giottoPoints object
y	Not used.
...	additional parameters to pass
point_size	size of points when plotting giottoPoints
type	what to plot: either 'poly' (default) or polygon 'centroid'
feats	specific features to plot within giottoPoints object (defaults to NULL, meaning all available features)
raster	default = TRUE, whether to plot points as rasterized plot with size based on size param
raster_size	Default is 600. Only used when raster is TRUE

Functions

• plot(x = giottoImage, y = missing): Plot magick-based giottoImage object. ... param passes to plot_giottoImage_MG

• plot(x = giottoLargeImage, y = missing): Plot terra-based giottoLargeImage object. ... param passes to plot_giottoLargeImage

• plot(x = giottoPolygon, y = missing): Plot terra-based giottoPolygon object. ... param passes to plot

• plot(x = giottoPoints, y = missing): terra-based giottoPoint object. ... param passes to plot

• plot(x = spatLocsObj, y = missing): Plot a spatLocsObj

• plot(x = spatialNetworkObj, y = missing): Plot a spatialNetworkObj

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.