| ... | ... |
@@ -1,23 +1,84 @@ |
| 1 |
+##' Correlation plot |
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+##' |
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+##' Visualize correlations between samples or features. All values in a |
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+##' correlation matrix are visualized by rectangles. |
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+##' |
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+##' @param x A matrix or \linkS4class{poplin} object.
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+##' @param poplin_in Name of a data matrix to retrieve. |
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+##' @param unit A character string specifying whether a correlation matrix is |
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+##' computed based on samples or features. One of "sample" or "feature". |
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+##' @param use A method for computing correlations in the presence of missing |
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+##' values. Refer to \code{?cor} for details.
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+##' @param method A character string specifying which correlation coefficient is |
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+##' to be computed. Refer to \code{?cor} for details.
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+##' @param widths Relative widths of heatmap and dendrogram. |
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+##' @param heights Relative heights of heatmap and dendrogram. |
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+##' @param colors A vector of colors for heatmap. |
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+##' @param grid_gap Gap between cells. |
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+##' @param hide_colorbar Logical controlling whether the color bar (legend) is |
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+##' hidden. |
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+##' @param showticklabels A logical vector of length 2 (x-axis, y-axis). If |
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+##' \code{FALSE}, the ticks are removed from the side of the plot.
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+##' @param row_dend_left Logical controlling whether the row dendrogram is |
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+##' placed on the left on the plot. |
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+##' @param ... Additional arguments passed to [heatmaply::heatmaply]. |
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+##' @return \code{gtable} of aligned plots.
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+##' @name poplin_corplot |
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+NULL |
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+ |
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+ |
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| 1 | 30 |
##' @export |
| 2 | 31 |
poplin_corplot <- function(x, ...) {
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| 3 | 32 |
UseMethod("poplin_corplot")
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| 4 | 33 |
} |
| 5 | 34 |
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+##' @rdname poplin_corplot |
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| 6 | 36 |
##' @export |
| 7 | 37 |
##' @importFrom heatmaply ggheatmap |
| 8 |
-poplin_corplot.default <- function(x, |
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+poplin_corplot.default <- function(x, unit = c("sample", "feature"),
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| 9 | 39 |
use = c("everything", "all.obs", "complete.obs",
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| 10 | 40 |
"na.or.complete", "pairwise.complete.obs"), |
| 11 | 41 |
method = c("pearson", "kendall", "spearman"),
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- showticklabels = c(TRUE, TRUE), ...) {
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+ widths = NULL, heights = NULL, |
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+ colors = viridis::viridis(n = 256, alpha = 1, |
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+ begin = 0, end = 1, |
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+ option = "viridis"), |
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+ grid_gap = 0, |
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+ hide_colorbar = FALSE, showticklabels = c(TRUE, TRUE), |
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+ row_dend_left = FALSE, ...) {
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+ unit <- match.arg(unit) |
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| 13 | 50 |
use <- match.arg(use) |
| 14 | 51 |
method <- match.arg(method) |
| 52 |
+ if (unit == "feature") {
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+ x <- t(x) |
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+ } |
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| 15 | 55 |
m <- cor(x, use = use, method = method) |
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- ggheatmap(m, showticklabels = showticklabels, ...) |
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+ ggheatmap(m, widths = widths, heights = heights, |
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+ grid_gap = grid_gap, colors = colors, |
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+ hide_colorbar = hide_colorbar, showticklabels = showticklabels, |
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+ row_dend_left = row_dend_left, ...) |
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| 17 | 60 |
} |
| 18 | 61 |
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+ |
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+##' @rdname poplin_corplot |
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| 19 | 64 |
##' @export |
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-poplin_corplot.poplin <- function(x, poplin_in , ...) {
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+poplin_corplot.poplin <- function(x, poplin_in , unit = c("sample", "feature"),
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+ use = c("everything", "all.obs",
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+ "complete.obs", "na.or.complete", |
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+ "pairwise.complete.obs"), |
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+ method = c("pearson", "kendall", "spearman"),
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+ widths = NULL, heights = NULL, |
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+ colors = viridis::viridis(n = 256, alpha = 1, |
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+ begin = 0, end = 1, |
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+ option = "viridis"), |
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+ grid_gap = 0, |
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+ hide_colorbar = FALSE, |
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+ showticklabels = c(TRUE, TRUE), |
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+ row_dend_left = FALSE, ...) {
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| 21 | 78 |
m <- .verify_and_extract_input(x, poplin_in) |
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- poplin_corplot.default(m, ...) |
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+ poplin_corplot.default(m, use = use, method = method, |
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+ widths = widths, heights = heights, |
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+ colors = colors, hide_colorbar = hide_colorbar, |
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+ showticklabels = showticklabels, |
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+ row_dend_left = row_dend_left, ...) |
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| 23 | 84 |
} |
| ... | ... |
@@ -7,17 +7,17 @@ |
| 7 | 7 |
##' @param x A matrix or \linkS4class{poplin} object.
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| 8 | 8 |
##' @param poplin_in Name of a data matrix to retrieve. |
| 9 | 9 |
##' @param widths Relative widths of heatmap and dendrogram. |
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-##' @param height Relative height of heatmap and dendrogram. |
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-##' @param grid_gap Gap between cells. |
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+##' @param heights Relative heights of heatmap and dendrogram. |
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| 12 | 11 |
##' @param colors A vector of colors for heatmap. |
| 12 |
+##' @param grid_gap Gap between cells. |
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| 13 | 13 |
##' @param hide_colorbar Logical controlling whether the color bar (legend) is |
| 14 | 14 |
##' hidden. |
| 15 | 15 |
##' @param showticklabels A logical vector of length 2 (x-axis, y-axis). If |
| 16 |
-##' \code{FALSE}, ticks are removed from the side of the plot.
|
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+##' \code{FALSE}, the ticks are removed from the side of the plot.
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| 17 | 17 |
##' @param row_dend_left Logical controlling whether the row dendrogram is |
| 18 | 18 |
##' placed on the left on the plot. |
| 19 | 19 |
##' @param ... Additional arguments passed to [heatmaply::heatmaply]. |
| 20 |
-##' @return gtable of aligned plot. |
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+##' @return \code{gtable} of aligned plots.
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| 21 | 21 |
##' @name poplin_naplot |
| 22 | 22 |
NULL |
| 23 | 23 |
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| ... | ... |
@@ -30,10 +30,11 @@ poplin_naplot <- function(x, ...) {
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| 30 | 30 |
##' @export |
| 31 | 31 |
##' @importFrom heatmaply is.na10 heatmaply |
| 32 | 32 |
poplin_naplot.default <- function(x, widths = NULL, heights = NULL, |
| 33 |
- grid_gap = 1, colors = viridis::viridis(2), |
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- hide_colorbar = TRUE, showticklabels = c(TRUE, FALSE), |
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- row_dend_left = FALSE, ...) {
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- p <- heatmaply(is.na10(x), grid_gap = grid_gap, colors = colors, |
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+ colors = viridis::viridis(2), grid_gap = 1, |
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+ hide_colorbar = TRUE, |
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+ showticklabels = c(TRUE, FALSE), |
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+ row_dend_left = FALSE, ...) {
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+ p <- heatmaply(is.na10(x), colors = colors, grid_gap = grid_gap, |
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| 37 | 38 |
showticklabels = showticklabels, |
| 38 | 39 |
row_dend_left = row_dend_left, |
| 39 | 40 |
return_ppxpy = TRUE, plot_method = "ggplot", ...) |
| ... | ... |
@@ -48,13 +49,13 @@ poplin_naplot.default <- function(x, widths = NULL, heights = NULL, |
| 48 | 49 |
##' @rdname poplin_naplot |
| 49 | 50 |
##' @export |
| 50 | 51 |
poplin_naplot.poplin <- function(x, poplin_in, widths = NULL, heights = NULL, |
| 51 |
- grid_gap = 1, color = viridis::viridis(2), |
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+ color = viridis::viridis(2), grid_gap = 1, |
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| 52 | 53 |
hide_colorbar = TRUE, |
| 53 | 54 |
showticklabels = c(TRUE, FALSE), |
| 54 | 55 |
row_dend_left = FALSE, ...) {
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| 55 | 56 |
m <- .verify_and_extract_input(x, poplin_in) |
| 56 | 57 |
poplin_naplot.default(m, widths = widths, heigths = heights, |
| 57 |
- grid_gap = grid_gap, color = color, |
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+ color = color, grid_gap = grid_gap, |
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| 58 | 59 |
hide_colorbar = hide_colorbar, |
| 59 | 60 |
showticklabels = showticklabels, |
| 60 | 61 |
row_dend_left = row_dend_left, ...) |
