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.
Examples
if (FALSE) { # \dontrun{
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)
} # }