view_gene_expression: view_gene_expression

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

view_gene_expression

Description

View gene expression in spatial omics data, in specific territories or the expression of genes in a subset of cells.

Usage

view_gene_expression(
  vesalius_assay,
  genes = NULL,
  norm_method = "last",
  trial = "last",
  territory_1 = NULL,
  territory_2 = NULL,
  cells = NULL,
  norm = TRUE,
  as_layer = FALSE,
  with_background = FALSE,
  cex = 10,
  cex_pt = 1,
  alpha = 0.75,
  max_size = 5,
  return_as_list = FALSE
)

Arguments

vesalius_assay	a vesalius_assay object
genes	character vector containing the genes you wish to visualise.
norm_method	character string - which count matrix should be used.
trial	character string describing which segmentation trial to use. Default is "last" which is the last trial used.
territory_1	integer or vector of integers descrbing territories in group 1 (see details)
territory_2	integer or vector of integers descrbing territories in group 2 (see details)
cells	charactor vector containing barcodes/spatial_indices associated with cell types of interest (see details)
norm	logical indicating if expression should be min/max normalised
as_layer	logical indicating if expression should represented as a territory/ layer.
cex	numeric - font size modulator
cex_pt	numeric point size
alpha	point transparency
return_as_list	logical - should plot be returned as simple list or as a ggplot object (single gene)/ patchwork object (multiple genes)

Details

Vesalius offers a plotting function that allows you to visualise gene expression.

This function offers multiple options depending on what you provide.

1. Overall expression You can visualise the overall expression pattern of a set of genes by providing a vesalius_assay object containing counts. If as_layer is set to FALSE this will show the expression at each sptial index indivdually. If set to TRUE, this will show the average expression on a gene in all territories present.

2. Expression in a territory You can visualise the expression of a gene in an isolated territory.

3. Expression of cells in one or more territory If you want to visualise the expression of specific cells, you can parse a character vector containing your cells of interest. This function will automatically subset the relevant territory data and show the expression only in the spatial indeces hat are associated with your cell type of interest. You can use this option to contrast the expression of cells between territories by also providing which territories you wish to contrast ('territory_1' and 'territory_2'). If only a single territory is provided, vesalius will only shows cell in that territory.

If you provide more than one gene, 'view_gene_expression' will return a ggarrange list containing all your genes as individual plots.

Value

a 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)

# simple smoothing
ves <- smooth_image(ves, dimensions = seq(1, 30))

# quick segmentation
ves <- segment_image(ves, dimensions = seq(1, 30))

# isolate territories
ves <- isolate_territories(ves)

# view over all expression
p <- view_gene_expression(ves, genes = "Malat1")
p1 <- view_gene_expression(ves, genes = "Malat1", as_layer = TRUE)

# view expression in isolated territory 
p2 <- view_gene_expression(ves, genes = "Malat1", territory_1 = 5)

# view expression of cells
cells <- sample(colnames(get_counts(ves)),300)
p3 <- view_gene_expression(ves,
 genes = "Malat",
 cells = cells,
 territory_1 = 5,
 terriotry_2 = 8)

## End(Not run)

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