In this vignette we will use an inForm data file that’s already been formatted for SPIAT with format_image_to_spe(), which we can load with data(). We will use define_celltypes() to define the cells with certain combinations of markers.


# define cell types
formatted_image <- define_celltypes(
    categories = c("Tumour_marker","Immune_marker1,Immune_marker2", 
                   "Immune_marker1,Immune_marker2,Immune_marker4", "OTHER"), 
    category_colname = "Phenotype", 
    names = c("Tumour", "Immune1", "Immune2", "Immune3", "Others"),
    new_colname = "Cell.Type")

We will be performing some basic analyses on this image. Here is the visualisation of the cell coordinates.

my_colors <- c("red", "blue", "darkcyan", "darkgreen")
plot_cell_categories(spe_object = formatted_image, 
                     categories_of_interest = 
                       c("Tumour", "Immune1", "Immune2", "Immune3"), 
                     colour_vector = my_colors, 
                     feature_colname = "Cell.Type")