measure_association_to_cell_properties

Plots the density or boxplot of a property of two cell celltypes or compares using t test/wilcoxon rank sum test.

measure_association_to_cell_properties(
  spe_object,
  property = "Cell.Area",
  celltypes,
  feature_colname = "Cell.Type",
  method = "density",
  Nucleus.Ratio = FALSE,
  log.scale = FALSE
)

Arguments

spe_object

SpatialExperiment object in the form of the output of format_image_to_spe.

property

String that is the name of the column of interest.

celltypes

String Vector of celltypes of interest.

feature_colname

String that speficies the column of the cell types.

method

String. The analysis to perform on the selected cell types and property. Options are "density", "box", "t", "wilcox".

Nucleus.Ratio

Boolean whether the ratio of the nucleus size is of interest.

log.scale

Boolean whether to log the data.

Value

With method "box" or "density a plot is returned. With method "t" or "wilcox", the text output from the test are returned.

Examples

measure_association_to_cell_properties(image_no_markers,
                                      celltypes = c("Tumour", "Immune1"),
                                      feature_colname = "Cell.Type",
                                      property = "Cell.Size",
                                      method = "box")

measure_association_to_cell_properties(image_no_markers,
                                      celltypes = c("Tumour", "Immune2"),
                                      feature_colname="Cell.Type",
                                      property = "Cell.Size",
                                      method = "t")
#> 
#> 	Welch Two Sample t-test
#> 
#> data:  Tumour and Immune2
#> t = 27.397, df = 230.97, p-value < 2.2e-16
#> alternative hypothesis: true difference in means is not equal to 0
#> 95 percent confidence interval:
#>  5.448048 6.292373
#> sample estimates:
#> mean of x mean of y 
#> 14.797360  8.927149 
#>