R/flowstyle_plot.R

In jspaezp/sctree: Tree based analysis of single rna-seq clusters

#' Plots data as faceted scatterplot emulating the ouput of flow cytometry
#'
#' Simulates flow cytometry plots for single cell rna seq data
#'
#' Note that it imputes a little bit of noise to values of 0 just for the
#' Sake of visualization
#'
#' @param object data, either a Seurat of a data frame object
#' @param markernames names of the markers to be used for the plot
#' @param classif_col name of the classification column to be used for
#'     the grouping, defaults to "ident"
#' @param warn logical indicating if warninf should be shown, defaults to TRUE
#' @param highlight_class a character indicating a class if it wants to be highlighted. ie "1"
#' @param ... additional argumetns to be passed to GGally::ggpairs
#'
#' @return a ggplot grid with the plots
#' @export
#'
#' @examples
#' plot_flowstyle(Seurat::pbmc_small, c("ACRBP", "TSC22D1", "VDAC3"))
plot_flowstyle <- function(object, markernames, classif_col = "ident", ...) {
    # TODO add argument to change to natural scale ...
    UseMethod("plot_flowstyle", object)
}


#' @importFrom GGally ggpairs wrap
#' @importFrom ggplot2 aes_string theme_bw
#' @importFrom stats rnorm
#' @describeIn plot_flowstyle Draw a flowstyle plot from a data.frame
#' @export
plot_flowstyle.data.frame <- function(object,
                                      markernames,
                                      classif_col = "ident",
                                      warn = TRUE,
                                      highlight_class = NULL,
                                      ...) {

    tmp_ident <- object[[classif_col]]
    object <- object[,markernames]

    # TODO add argument decide when to add noise to the dataset ...
    object[object == 0] <- abs(stats::rnorm(sum(object == 0),mean = 0, sd = 0.2))
    object$ident <- tmp_ident

    if (warn & length(unique(object$ident)) > 5 & is.null(highlight_class)) {
        warning("There are more than 5 different identities, ",
                "telling them appart might be hard based on color only. ",
                "Consider using the 'highlight_class' argument")
    }

    columns_plot <-  1:(ncol(object) - 1)
    aes <- ggplot2::aes_string(colour = "ident")

    if (!is.null(highlight_class)) {
        object$highlight <- object$ident %in% highlight_class
        aes <- ggplot2::aes_string(colour = "ident", alpha = "highlight")
    }

    suppressWarnings({
        g <- GGally::ggpairs(
            as.data.frame(object),
            columns = columns_plot,
            aes,
            progress = FALSE,
            lower = list(
                continuous = GGally::wrap(
                    "dot_no_facet")),
            diag = list(
                continuous = GGally::wrap(
                    'densityDiag',
                    alpha = 0.3)),
            upper = list(
                continuous =  GGally::wrap(
                    "density",
                    alpha = 0.4)), ...) +
            ggplot2::theme_bw()
    })

    return(g)
}


#' @describeIn plot_flowstyle Draw a flowstyle plot from a Seurat object
#' @export
plot_flowstyle.Seurat <- function(object, markernames, classif_col = "ident", ...) {
    tmp <- as.data.frame.Seurat(object, markernames, FALSE)
    plot_flowstyle.data.frame(
        tmp, markernames = markernames,
        classif_col = classif_col, ...)
}