R/plot_distance_heatmap.R

In TrigosTeam/SPIAT: Spatial Image Analysis of Tissues

#' plot_distance_heatmap
#'
#' @description Takes the output of cell_distances and plot the distances as a
#'   heatmap.
#'
#' @param phenotype_distances_result Dataframe output from
#'   `calculate_summary_distances_between_celltypes` or
#'   `calculate_minimum_distances_between_celltypes`.
#' @param metric Metric to be plotted. One of "mean", "std.dev", "median", "min"
#'   or "max".
#' @import ggplot2
#' @return A plot is returned
#' @examples
#' dists <- calculate_pairwise_distances_between_celltypes(SPIAT::defined_image, 
#' cell_types_of_interest = c("Tumour","Immune1"), feature_colname = "Cell.Type")
#' summary_distances <- calculate_summary_distances_between_celltypes(dists)
#' plot_distance_heatmap(summary_distances)
#' @export

plot_distance_heatmap <- function(phenotype_distances_result, metric = "mean"){
    
    # setting these variables to NULL as otherwise get "no visible binding for global variable" in R check
    Reference <- Target <- Min <- Max <- Mean <- Std.Dev <- Median <- NULL
    
    if(metric == "mean"){
        limit <- range(unlist(phenotype_distances_result$Mean), na.rm=TRUE)
        g <- ggplot(phenotype_distances_result, aes(x = Reference, y = Target, fill = Mean)) +
            geom_tile() +
            xlab("Reference cell type") +
            ylab("Target cell type") +
            theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_rect(fill = "white"),
                  axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5)) +
            scale_fill_viridis_c(limits = limit, direction = -1)
        # methods::show(g)
        
    }else if(metric == "std.dev"){
        limit <- range(unlist(phenotype_distances_result$Std.Dev), na.rm=TRUE)
        g <- ggplot(phenotype_distances_result, aes(x = Reference, y = Target, fill = Std.Dev)) + geom_tile() + 
            xlab("Reference cell type") + ylab("Target cell type") +
            theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_rect(fill = "white"),
                  axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5)) +
            scale_fill_viridis_c(limits = limit, direction = -1)
        # methods::show(g)
        
    }else if(metric == "median"){
        limit <- range(unlist(phenotype_distances_result$Median), na.rm=TRUE)
        g <- ggplot(phenotype_distances_result, aes(x = Reference, y = Target, fill = Median)) + geom_tile() + 
            xlab("Reference cell type") + ylab("Target cell type") +
            theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_rect(fill = "white"),
                  axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5)) +
            scale_fill_viridis_c(limits = limit, direction = -1)
        # methods::show(g)
    }else if(metric == "min"){
        limit <- range(unlist(phenotype_distances_result$Min), na.rm=TRUE)
        g <- ggplot(phenotype_distances_result, aes(x = Reference, y = Target, fill = Min)) + geom_tile() + 
            xlab("Reference cell type") + ylab("Target cell type") +
            theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_rect(fill = "white"),
                  axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5)) +
            scale_fill_viridis_c(limits = limit, direction = -1)
        # methods::show(g)
    }else if(metric == "max"){
        limit <- range(unlist(phenotype_distances_result$Max), na.rm=TRUE)
        g <- ggplot(phenotype_distances_result, aes(x = Reference, y = Target, fill = Max)) + geom_tile() + 
            xlab("Reference cell type") + ylab("Target cell type") +
            theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_rect(fill = "white"),
                  axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5)) +
            scale_fill_viridis_c(limits = limit, direction = -1)
        # methods::show(g)
    }
    return(g)
}