visualize_genes: This function visualizes the results of the clustering and...

In tmirus/TTT: What the Package Does (One Line, Title Case)

Description

This function visualizes the results of the clustering and analysis using spatial plots and heatmaps

Usage

visualize_genes(
  counts,
  ids,
  img = NULL,
  clustering,
  genelist,
  filepath = NULL,
  plot.params = list(nx = 35, ny = 33, ox = 0, oy = 0)
)

Arguments

counts	non-negative numeric matrix containing gene counts, rows correspond to spots, columns correspond to genes
ids	data frame or matrix assigning spatial coordinates to the spots
img	image of ST slide, read using EBImage::readImage()
clustering	numeric vector, same order as rownames(counts), assigning each spot a cluster
genelist	data frame containing genes of interest (e.g. output of filter_genes)
filepath	character, directory in which to save plots; if not specified, plots will not be saved to disk
plot.params	plotting parameters as returned by plot_adjustment()

Value

list containing 4 plots (ggplot objects):

1. spatial.cluster - overlay of clustering on ST image if image was supplied; NULL otherwise
   

2. spatial.cluster.legend - spatial clustering, without ST image in background, but with legend
   

3. heatmap.plt - simplified heatmap, depicting mean expression of all interesting genes in the different clusters
   

4. heatmap.full.plt - heatmap visualizing expression of all interesting genes in all spots
   

tmirus/TTT documentation built on April 17, 2021, 11:04 p.m.