image_plot: image_plot - plotting vesalius embeddings

In patrickCNMartin/Vesalius: Vesalius: Dissecting Tissue Anatomy from Spatial Transcriptomic Data

image_plot - plotting vesalius embeddings

Description

image_plot - plotting vesalius embeddings

Usage

image_plot(
  vesalius_assay,
  dimensions = seq(1, 3),
  embedding = "last",
  cex = 10
)

Arguments

vesalius_assay	a vesalius_assay object
dimensions	which dimensions to use to generate image (see details)
embedding	character string descrining which embedding should be used for image generation.
cex	numeric - font and point size resizing factor.

Details

Once you have generated your embeddings, you can visualise these embeddings using the image_plot function. This function will generate a ggplot object representing the embedding image containing all pixels. You can select any dimension and in any combination you desire, however you can only select 1 or 3 dimensions to visualise at a time. This will either generate grey scale image or RGB images.

This function is always applied to the active embedding. By default, this is the last you generated. This means that you can also use this function to visualise the effect if smoothing, equalization, regularisation or segmentation.

Please note that if you are using "louvain" or "leiden" for image segmentation, this will always generate grey scale images even if you select multiple dimensions. "Kmeans" on the other hand will still produce RGB color segments.

The usage of this function remains the same in after any processing steps.

Value

ggplot object

Examples

## Not run: 
data(vesalius)
# First we build a simple object
ves <- build_vesalius_object(coordinates, counts)
# We can do a simple run 
ves <- build_vesalius_embeddings(ves)
# Plot 1st 3 PCs
p <- image_plot(ves)


## End(Not run)

patrickCNMartin/Vesalius documentation built on April 17, 2025, 11:31 p.m.