measure_association_to_cell_properties

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

measure_association_to_cell_properties(
  sce_object,
  property = "Cell.Area",
  phenotypes,
  merge = NULL,
  merge_name = NULL,
  method = "density",
  Nucleus.Ratio = FALSE,
  log.scale = FALSE
)

Arguments

sce_object	SingleCellExperiment object in the form of the output of format_image_to_sce
property	String that is the name of the column of interest
phenotypes	Vector of phenotypes of interest
merge	Vector of phenotypes to be merged
merge_name	String that is the name of the merged phenotype
method	the analysis to do on the selected phenotypes and property. Options are density, box, t, wilcox
Nucleus.Ratio	when the ratio of the nucleus size is of interest
log.scale	if 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(SPIAT::formatted_image,
                                      phenotypes = c("CD3,CD4", "CD3,CD8"),
                                      property = "Cell.Area",
                                      method = "box")
measure_association_to_cell_properties(SPIAT::formatted_image,
                                      phenotypes = c("CD3,CD4", "CD3,CD8"),
                                      property = "Cell.Area",
                                      method = "t")                                     
#> 
#> 	Welch Two Sample t-test
#> 
#> data:  CD3,CD4 and CD3,CD8
#> t = 2.1766, df = 259.32, p-value = 0.03041
#> alternative hypothesis: true difference in means is not equal to 0
#> 95 percent confidence interval:
#>   2.783879 55.630562
#> sample estimates:
#> mean of x mean of y 
#>  369.1637  339.9565 
#>