Added plotXY to re-use scater's aesthetics for arbitrary x/y plots.

NAMESPACE

@@ -67,6 +67,7 @@ export(plotRowData)
 export(plotScater)
 export(plotTSNE)
 export(plotUMAP)
+export(plotXY)
 export(projectReducedDim)
 export(quickPerCellQC)
 export(readSparseCounts)

R/plotXY.R

@@ -0,0 +1,140 @@
+#' Plot arbitrary x- and y-coordinates
+#'
+#' Reuse \pkg{scater}'s plotting machinery for arbitrary x- and y-coordinates.
+#' This allows users to maintain the same aesthetic style when creating plots outside of a \link[SingleCellExperiment]{SingleCellExperiment}.
+#'
+#' @param x Vector containing the x-coordinates.
+#' Alternatively, a data.frame with a single column.
+#' Alternatively \code{NULL}, in which case all points are assumed to have the same categorical x-coordinate.
+#' @param y Vector containing the y-coordinates, of same length as \code{x}.
+#' Alternatively, a data.frame with a single column.
+#' @param colour_by Vector containing a variable to colour by, of the same length as \code{x}.
+#' Alternatively, a data.frame with a single column.
+#' @param shape_by Vector containing a variable to shape by, of the same length as \code{x}.
+#' Alternatively, a data.frame with a single column.
+#' @param size_by Vector containing a variable to shape by, of the same length as \code{x}.
+#' Alternatively, a data.frame with a single column.
+#' @param other_fields A data frame of additional columns to add to the data.frame passed to \pkg{ggplot2}.
+#' This should have number of rows equal to the length of \code{y}.
+#' Alternatively, a named list of vectors of length equal to that of \code{y}.
+#' @inheritParams plotColData
+#'
+#' @return A \link{ggplot} object.
+#'
+#' @author Aaron Lun
+#'
+#' @examples
+#' x <- runif(100)
+#' y <- rnorm(100)
+#'
+#' # Manually add labels.
+#' plotXY(x, y) + ggplot2::xlab("X") + ggplot2::ylab("Y")
+#'
+#' # Insert labels via data frames.
+#' plotXY(data.frame(foo=x), data.frame(bar=y))
+#'
+#' col <- sample(LETTERS, length(x), replace=TRUE)
+#' plotXY(x, y, colour_by=col) + guides(color=guide_legend("stuff"))
+#'
+#' shape <- sample(LETTERS[1:5], length(x), replace=TRUE)
+#' plotXY(x, y, shape=data.frame(FOO=shape))
+#'
+#' size <- runif(length(x))
+#' plotXY(x, y, size=data.frame(BAR=size))
+#'
+#' plotXY(x, y, other_fields=data.frame(stuff = rbinom(100, 1, 0.5) > 0)) +
+#'     ggplot2::facet_grid(~stuff)
+#'
+#' @export
+plotXY <- function(
+    x,
+    y,
+    colour_by = color_by,
+    shape_by = NULL,
+    size_by = NULL,
+    order_by = NULL,
+    other_fields = list(),
+    swap_rownames = NULL,
+    color_by = NULL,
+    point_fun = NULL,
+    scattermore = FALSE,
+    bins = NULL,
+    summary_fun = "sum",
+    hex = FALSE,
+    ...
+) {
+    ylab <- NULL
+    if (is.data.frame(y) || is(y, "DataFrame")) {
+        stopifnot(ncol(y) == 1L)
+        ylab <- colnames(y)
+        y <- y[,1]
+    }
+
+    df_to_plot <- data.frame(Y = y)
+
+    xlab <- NULL
+    if (is.null(x)) {
+        df_to_plot$X <- factor(character(nrow(df_to_plot)))
+    } else if (is.data.frame(x) || is(x, "DataFrame")) {
+        stopifnot(ncol(y) == 1L)
+        xlab <- colnames(x)
+        df_to_plot$X <- x[,1]
+    } else {
+        df_to_plot$X <- x
+    }
+
+    if (!is.null(colour_by)) {
+        if (is.data.frame(colour_by) || is(colour_by, "DataFrame")) {
+            stopifnot(ncol(colour_by) == 1)
+            df_to_plot$colour_by <- colour_by[,1]
+            colour_by <- colnmames(colour_by)
+        } else {
+            df_to_plot$colour_by <- colour_by
+            colour_by <- "colour"
+        }
+    }
+
+    if (!is.null(size_by)) {
+        if (is.data.frame(size_by) || is(size_by, "DataFrame")) {
+            stopifnot(ncol(size_by) == 1)
+            df_to_plot$size_by <- size_by[,1]
+            size_by <- colnames(size_by)
+        } else {
+            df_to_plot$size_by <- size_by
+            size_by <- "size"
+        }
+    }
+
+    if (!is.null(shape_by)) {
+        if (is.data.frame(shape_by) || is(shape_by, "DataFrame")) {
+            stopifnot(ncol(shape_by) == 1)
+            df_to_plot$shape_by <- shape_by[,1]
+            shape_by <- colnames(shape_by)
+        } else {
+            df_to_plot$shape_by <- shape_by
+            shape_by <- "shape"
+        }
+    }
+
+    if (length(other_fields)) {
+        if (!is.data.frame(other_fields) && !is(other_fields, "DataFrame")) {
+            other_fields <- do.call(data.frame, other_fields)
+        }
+        df_to_plot <- cbind(df_to_plot, other_fields)
+    }
+
+    .central_plotter(
+        df_to_plot, 
+        xlab = xlab,
+        ylab = ylab,
+        colour_by = colour_by,
+        size_by = size_by,
+        shape_by = shape_by,
+        scattermore = scattermore,
+        bins = bins,
+        summary_fun = summary_fun,
+        hex = hex,
+        ...,
+        point_FUN = point_fun
+    )
+}