image_splitter: Split a large image into sub images

In TrigosTeam/SPIAT: Spatial Image Analysis of Tissues

Split a large image into sub images

Description

Takes in an image in SpatialExperiment format, splits the image into specified sections and returns a list of SpatialExperiment objects. Users can choose to plot the cell positions in each sub image. Note that this function does not split the assay.

Usage

image_splitter(
  spe_object,
  number_of_splits,
  plot = FALSE,
  cut_labels = TRUE,
  colour_vector = NULL,
  minX = NULL,
  maxX = NULL,
  minY = NULL,
  maxY = NULL,
  feature_colname = "Phenotype"
)

Arguments

spe_object	'SpatialExperiment' object in the form of the output of format_image_to_spe.
number_of_splits	Numeric. specifying the number of segments (e.g. 2 = 2x2, 3 = 3x3).
plot	Boolean. Specifies whether the splitted images should be printed in a pdf.
cut_labels	Boolean. Specifies whether to plot where the image had been segmented.
colour_vector	String Vector. If specified, the colours will be used for plotting. If NULL, colors will be generated automatically.
minX	Integer used to specify the minimum x boundary to be splitted.
maxX	Integer used to specify the maximum x boundary to be splitted.
minY	Integer used to specify the minimum y boundary to be splitted.
maxY	Integer used to specify the maximum y boundary to be splitted.
feature_colname	String specifying which column the colouring should be based on. Specify when 'plot' is TRUE. Default is "Phenotype".

Value

A list of spe objects is returned. Each data frame represents an image without assay data.

Examples

split_image <- image_splitter(SPIAT::simulated_image, number_of_splits=3, 
plot = FALSE)

TrigosTeam/SPIAT documentation built on Aug. 22, 2024, 7:50 p.m.