R/plotRowData.R

In LTLA/scater: Single-Cell Analysis Toolkit for Gene Expression Data in R

#' Plot row metadata
#'
#' Plot row-level (i.e., gene) metadata from a SingleCellExperiment object.
#'
#' @param object A SingleCellExperiment object containing expression values and experimental information.
#' @param y String specifying the column-level metadata field to show on the y-axis.
#' Alternatively, an \link{AsIs} vector or data.frame, see \code{?\link{retrieveFeatureInfo}}.
#' @param x String specifying the column-level metadata to show on the x-axis.
#' Alternatively, an \link{AsIs} vector or data.frame, see \code{?\link{retrieveFeatureInfo}}.
#' If \code{NULL}, nothing is shown on the x-axis.
#' @param colour_by Specification of a row metadata field or a cell to colour by, see \code{?\link{retrieveFeatureInfo}} for possible values. 
#' @param shape_by Specification of a row metadata field or a cell to shape by, see \code{?\link{retrieveFeatureInfo}} for possible values. 
#' @param size_by Specification of a row metadata field or a cell to size by, see \code{?\link{retrieveFeatureInfo}} for possible values. 
#' @param by.assay.type A string or integer scalar specifying which assay to obtain expression values from, 
#' for use in point aesthetics - see \code{?\link{retrieveFeatureInfo}} for details.
#' @param other_fields Additional feature-based fields to include in the data.frame, see \code{?"\link{scater-plot-args}"} for details.
#' @param color_by Alias to \code{colour_by}.
#' @param by_exprs_values Alias to \code{by.assay.type}.
#' @param ... Additional arguments for visualization, see \code{?"\link{scater-plot-args}"} for details.
#'
#' @details 
#' If \code{y} is continuous and \code{x=NULL}, a violin plot is generated.
#' If \code{x} is categorical, a grouped violin plot will be generated, with one violin for each level of \code{x}.
#' If \code{x} is continuous, a scatter plot will be generated.
#'
#' If \code{y} is categorical and \code{x} is continuous, horizontal violin plots will be generated.
#' If \code{x} is missing or categorical, rectangule plots will be generated where the area of a rectangle is proportional to the number of points for a combination of factors.
#'
#' @return A \link{ggplot} object.
#'
#' @examples
#' example_sce <- mockSCE()
#' example_sce <- logNormCounts(example_sce)
#' rowData(example_sce) <- cbind(rowData(example_sce), 
#'     perFeatureQCMetrics(example_sce))
#' 
#' plotRowData(example_sce, y="detected", x="mean") +
#'     scale_x_log10()
#'
#' @export
plotRowData <- function(object, y, x = NULL, 
    colour_by = color_by, shape_by = NULL, size_by = NULL, 
    by_exprs_values = "logcounts", other_fields = list(), color_by = NULL,
    by.assay.type=by_exprs_values,    
    ...)
{
    if (!is(object, "SingleCellExperiment")) {
        stop("object must be an SingleCellExperiment object.")
    }

    ## Define dataframe to pass to plotMetadata
    y_by_out <- retrieveFeatureInfo(object, y, search = "rowData")
    y_lab <- y_by_out$name
    if (is.null(y_lab)) {
        stop(sprintf("could not find '%s' in 'rowData(object)'", y))
    }
    df_to_plot <- data.frame(Y=y_by_out$value)

    if (!is.null(x)) {
        x_by_out <- retrieveFeatureInfo(object, x, search = "rowData")
        x_lab <- x_by_out$name
        if (is.null(x_lab)) {
            stop(sprintf("could not find '%s' in 'rowData(object)'", x))
        }
        df_to_plot$X <- x_by_out$value
    } else {
        x_lab <- NULL
        df_to_plot$X <- factor(character(nrow(object)))
    }

    ## checking visualization arguments
    vis_out <- .incorporate_common_vis_row(df_to_plot, se = object, 
        colour_by = colour_by, shape_by = shape_by, size_by = size_by, 
        by.assay.type = by.assay.type, other_fields = other_fields)

    df_to_plot <- vis_out$df
    colour_by <- vis_out$colour_by
    shape_by <- vis_out$shape_by
    size_by <- vis_out$size_by

    # Creating the plot object:
    .central_plotter(df_to_plot, xlab = x_lab, ylab = y_lab,
                     colour_by = colour_by, size_by = size_by, shape_by = shape_by, 
                     ..., point_FUN=NULL)
}