R/d3heatmap.R
In rstudio/d3heatmap: Interactive Heat Maps Using 'htmlwidgets' and 'D3.js'
Defines functions
renderD3heatmap
d3heatmapOutput
encodeAsPNG
d3heatmap
Documented in
d3heatmap
d3heatmapOutput
renderD3heatmap
#' @import htmlwidgets
#' @importFrom grDevices col2rgb rgb colorRampPalette
#' @importFrom stats as.dendrogram dendrapply dist hclust is.leaf order.dendrogram reorder sd
#' @importFrom utils capture.output str
NULL
#' D3 Heatmap widget
#'
#' Creates a D3.js-based heatmap widget.
#'
#' @param x A numeric matrix or data.frame with numeric columns. All non-numeric columns
#' will be filtered out
#'
#' @param main \emph{string} Plot title. Defaults to \code{NULL}.
#'
#' @param theme A custom CSS theme to use. Currently the only valid values are
#' \code{""} and \code{"dark"}. \code{"dark"} is primarily intended for
#' standalone visualizations, not R Markdown or Shiny.
#'
#' @param col Either a colorbrewer2.org palette name (e.g. \code{"YlOrRd"}
#' or \code{"Blues"}), or a vector of colors to interpolate in hexadecimal
#' \code{"#RRGGBB"} format, or a color interpolation function like
#' \code{\link[grDevices]{colorRamp}}.
#'
#' @param breaks \emph{integer} Either a numeric vector indicating the splitting
#' points for binning x into colors, or a integer number of break points
#' to be used, in which case the break points will be spaced equally
#' between min(x) and max(x).
#'
#' @param symbreaks \emph{logical} Arrange color bins symmetrically around zero?
#'
#' @param Rowv determines if and how the row dendrogram
#' should be reordered. By default, it is TRUE, which implies
#' dendrogram is computed and reordered based on row means.
#' If NULL or FALSE, then no dendrogram is computed and no reordering
#' is done. If a dendrogram, then it is used "as-is", i.e. without any
#' reordering. If a vector of integers, then a dendrogram is computed
#' and reordered based on the order of the vector.
#'
#' @param Colv determines if and how the column dendrogram should be
#' reordered. Has the options as the Rowv argument above and additionally
#' when x is a square matrix, Colv = "Rowv" means that columns should be
#' treated identically to the rows.
#'
#' @param distfun function used to compute the distance (dissimilarity)
#' between both rows and columns. Defaults to dist.
#'
#' @param hclustfun function used to compute the hierarchical clustering
#' when Rowv or Colv are not dendrograms. Defaults to hclust.
#'
#' @param dendrogram character string indicating whether to draw 'none',
#' 'row', 'column' or 'both' dendrograms. Defaults to 'both'. However, if
#' Rowv (or Colv) is FALSE or NULL and dendrogram is 'both', then a warning
#' is issued and Rowv (or Colv) arguments are honored.
#'
#' @param reorderfun function(d, w) of dendrogram and weights for reordering
#' the row and column dendrograms. The default uses stats{reorder.dendrogram}
#'
#' @param k_row,kr an integer scalar with the desired number of groups by which
#' to color the dendrogram's branches in the rows
#' (uses \link[dendextend]{color_branches})
#'
#' @param k_col,kc an integer scalar with the desired number of groups by which
#' to color the dendrogram's branches in the columns
#' (uses \link[dendextend]{color_branches})
#'
#' @param print.values \emph{logical} Show the values inside the cells. Defaults to \code{FALSE}.
#'
#' @param key Show color key and density
#' information? \code{TRUE/FALSE}. Defaults to \code{FALSE}
#'
#' @param keysize \emph{numeric} value indicating the relative size of the key. Will multiple the labRowSize and labColSize.
#' Defaults to 1
#'
#' @param key.title Separate title for color key. Defaults to \code{NULL}.
#'
#' @param key.location \emph{Required, character} Location for color key, either \code{"fl", "br", "tr"
#' "tl", or "bl"} for "float", "bottom right", "top right", "top left", and "bottom left".
#' Defaults to \code{"fl"}, which follows the location of the axis labels.
#'
#' @param density.info \emph{Optional, character} indicating whether to superimpose
#' a 'histogram' or no plot ('none') on the color-key (legend).
#'
#' @param denscol \emph{Optional, character} giving the color for the density
#' display specified by 'density.info', defaults to \code{NULL} which will fill the
#' bars with the same color as the bin
#'
#' @param width Width in pixels (optional, defaults to automatic sizing).
#'
#' @param height Height in pixels (optional, defaults to automatic sizing).
#'
#' @param labColSize Size of axes, in pixels.
#'
#' @param labRowSize Size of axes, in pixels.
#'
#' @param cexCol Font size of column labels, as a scalar to '12px' font. Default to
#' 0.2 + 1/log10(ncol(x)).
#'
#' @param cexRow Font size of row labels, as a scalar to '12px' font size. Defaults to
#' 0.2 + 1/log10(nrow(x)).
#'
#' @param srtCol Angle of axis labels. Defaults to 60. Maximum of 90 (vertical), minimum of 25.
#'
#' @param sideCol,xaxis.location 3 or 1, for "bottom" or "top", which side column labels
#' display. Defaults to 3 ("bottom"). For \code{xaxis.location} use "bottom"
#' or "top".
#'
#' @param sideRow,yaxis.location 2 or 4, for "left" or "right", which side row labels
#' display. Defaults to 4 ("right"). For \code{yaxis.location} use "left" or "right".
#'
#' @param xlab Title text of x axis
#'
#' @param ylab Title text of y axis
#'
#' @param xaxis_title_font_size Font size of x axis title in pixels. Defaults to 14.
#'
#' @param yaxis_title_font_size Font size of y axis title in pixels. Defaults to 14.
#'
#' @param brush_color The base color to be used for the brush. The brush will be
#' filled with a low-opacity version of this color. \code{"#RRGGBB"} format
#' expected.
#'
#' @param show_grid \code{TRUE} to show gridlines, \code{FALSE} to hide them, or
#' a numeric value to specify the gridline thickness in pixels (can be a non-integer).
#'
#' @param anim_duration Number of milliseconds to animate zooming in and out.
#' For large \code{x} it may help performance to set this value to \code{0}.
#'
#' @param symm logical indicating if x should be treated symmetrically; can only be true when x is a square matrix.
#'
#' @param revC logical indicating if the column order should be reversed for plotting.
#' Default (when missing) - is FALSE, unless symm is TRUE.
#' This is useful for cor matrix.
#'
#' @param scale character indicating if the values should be centered and scaled in either
#' the row direction or the column direction, or none. The default is "none".
#'
#' @param scale.by.range logical indicating whether to scale rows or columns by
#' the range of each row and column. Setting this parameter to \code{TRUE}
#' automatically sets \code{na.rm} to \code{TRUE}
#'
#' @param na.rm logical indicating whether NA's should be removed.
#'
#' @param na.value numeric indicating where NA's should be substituted to trigger the NA color.
#'
#' @param na.color Color of NA values in heatmap. Defaults to neutral gray.
#'
#' @param rng A vector of two numbers, namely the minimum and maximum value
#' to use when determining the mapping from values to colors. This is useful
#' when the range of values changes between heatmaps, but colors should be the
#' same (optional, defaults to the minimum and maximum of \code{x}).
#'
#' @param digits \emph{integer} indicating the number of decimal places to be used by \link{round} for 'label'.
#'
#' @param notecol \emph{character} name or hex specifying the color of the values printed
#' inside the cells
#'
#' @param notecex,cex.note \emph{numeric} scalar of 12 to determine pixel size of printed cell values.
#' inside the cells. If not specified, the minimum font size between the x and y axes.
#'
#' @param cellnote_row \emph{character} Label to display next to the row value when the user hovers over the cell.
#' If not specified, tries to match the \code{xlab}; if no axis title, defaults to "Row".
#'
#' @param cellnote_col \emph{character} Label to display next to the column value when the user hovers over the cell.
#' If not specified, tries to match the \code{ylab}; if no axis title, defaults to "Col".
#'
#' @param cellnote_val \emph{character} Label to display next to the cell value when the user hovers over the cell.
#' Defaults to "Value".
#'
#' @param cellnote \emph{numeric} (optional) matrix of the same dimensions as \code{x} that has the human-readable version of each value, for displaying to the user on hover. If \code{NULL}, then \code{x} will be coerced using \code{\link{as.character}}.
#' If missing, it will use \code{x}, after rounding it based on the \code{digits} parameter.
#'
#' @param cellnote_scale \emph{logical} (default is FALSE). IF cellnote is missing and x is used, should cellnote be scaled if x is also scaled?
#'
#' @param labRow character vectors with row labels to use (from top to bottom); default to rownames(x).
#'
#' @param labCol character vectors with column labels to use (from left to right); default to colnames(x).
#'
#' @param ColSideColors (optional) character vector of length ncol(x), or matrix with
#' columns equal to ncol(x), containing the color names for a horizontal side bar that may
#' be used to annotate the columns of x. \code{ColIndividualColors}, from heatmap.2, can
#' also be used
#'
#' @param RowSideColors (optional) character vector of length nrow(x), or matrix with rows
#' equal to nrow(x), containing the color names for a vertical side bar that may be used to
#' annotate the rows of x. \code{RowIndividualColors}, from heatmap.3, can also be used
#'
#' @param RowColorsPalette a palette of colors to use for RowSideColors if passing a non-color matrix
#'
#' @param ColColorsPalette a palette of colors to use for ColSideColors if passing a non-color matrix
#'
#' @param RowColorsNames the names of the variables for RowSideColors. Overrides colnames(RowSideColors)
#'
#' @param ColColorsNames the names of the variables for ColSideColors. Overrides rownames(ColSideColors)
#' with rows equal to nrow(x), containing the color names for a vertical side bar that may be used to annotate the
#' rows of x.
#'
#' @param ... a catch for undocumented features or unused arguments from heatmap.2
#' or heatmap.3, to enable direct use of those formulations in d3heatmap
#'
#' @import htmlwidgets
#'
#' @source
#' The interface was designed based on \link{heatmap} and \link[gplots]{heatmap.2}
#'
#' @seealso
#' \link{heatmap}, \link[gplots]{heatmap.2}
#'
#' @examples
#' \dontrun{
#'
#' d3heatmap(mtcars, scale = "column", col = "Blues")
#'
#' }
#'
#' @export
d3heatmap <- function(x
, main = NULL
, width = NULL
, height = NULL
, show_grid = TRUE
, anim_duration = 500
, rng = NULL
## dendrogram control
, symm = FALSE
, Rowv = TRUE
, Colv = if (symm) "Rowv" else TRUE
, distfun = dist
, hclustfun = hclust
, dendrogram = c("both", "row", "column", "none")
, reorderfun = function(d, w) reorder(d, w)
, k_row = NULL
, k_col = NULL
, kr
, kc
, revC = NULL
## data scaling
, scale = c("none", "row", "column")
, scale.by.range = FALSE
, na.rm = TRUE
, na.color = "#777777"
, na.value = NA
## legend (color key)
, key = FALSE
, keysize = 1
, key.title = NULL
, key.location = c("fl", "br", "tr", "tl", "bl")
, density.info = c('histogram', 'none')
, denscol = NULL
## cellnote formatting
, digits = 3L
, cellnote = NULL
, cellnote_scale = FALSE
, cellnote_row = NULL
, cellnote_col = NULL
, cellnote_val = "Value"
, brush_color = "#0000FF"
, print.values = FALSE
, notecol = '#222222'
, notecex = 1
, cex.note
## color controls
, theme = NULL
, col = "RdYlBu"
, breaks = NULL
, symbreaks = FALSE
## axis controls
, labRow = rownames(x)
, labCol = colnames(x)
, labColSize = 80
, labRowSize = 120
, cexCol = NULL
, cexRow = NULL
, srtCol = 60
, sideCol = 3
, sideRow = 4
, xaxis.location
, yaxis.location
, xlab = NULL
, ylab = NULL
, xaxis_title_font_size = 14
, yaxis_title_font_size = 14
# side colors
, ColSideColors = NULL
, RowSideColors = NULL
, RowColorsPalette = NULL
, ColColorsPalette = NULL
, RowColorsNames = NULL
, ColColorsNames = NULL
, ...
) {
if(length(dim(x)) != 2) {
stop(paste("x is not a 2-dimensional object. Here is the str output of x:", capture.output(str(x)), collapse = "\n"))
}
if(is.matrix(x) && !is.numeric(x)) {
warning(paste(capture.output(str(x)), collapse = "\n"))
stop("d3heatmap data must be a numeric
matrix or a data.frame with numeric columns")
}
# we'll modify this to take any matrix or data.frame, but filter out all
# non-numeric columns
if (is.data.frame(x) | is.table(x))
x <- x[, sapply(x, is.numeric)]
opts <- list(...)
axis.locations <- c("top", "left", "bottom", "right")
## pre-process paraemters
##===========================================================
## process the overlap of parameters between the old d3heatmap,
## heatmap.2, and heatmap.3 APIs
if (!missing(kr)) k_row <- kr
if (!missing(kc)) k_col <- kc
if (!missing(cex.note)) notecex <- cex.note
if(!is.null(ColSideColors))
ColSideColors <- matrix(ColSideColors, ncol = ncol(x))
if(!is.null(RowSideColors))
RowSideColors <- matrix(RowSideColors, nrow = nrow(x))
if (!is.null(opts$ColIndividualColors))
ColSideColors <- matrix(opts$ColIndividualColors, ncol = ncol(x))
if (!is.null(opts$RowIndividualColors))
RowSideColors <- matrix(opts$RowIndividualColors, nrow = nrow(x))
if (is.null(RowColorsPalette))
RowColorsPalette <- c('blue', 'orange', 'black')
if (is.null(ColColorsPalette))
ColColorsPalette <- c('cyan', 'maroon', 'grey')
if (is.null(RowColorsNames)) RowColorsNames <- colnames(RowSideColors)
if (is.null(ColColorsNames)) ColColorsNames <- rownames(ColSideColors)
## additional controls for working with the gadget (shiny inputs)
##===========================================================
if (!is.null(k_row)) if (is.na(k_row)) k_row <- NULL
if (!is.null(k_col)) if (is.na(k_col)) k_col <- NULL
if (!is.null(cexCol)) if (is.na(cexCol)) cexCol <- NULL
if (!is.null(cexRow)) if (is.na(cexRow)) cexRow <- NULL
if(!missing(xaxis.location)) {
xaxis.location <- tolower(xaxis.location)
if (xaxis.location %in% c('top', 'bottom'))
sideCol <- which(axis.locations == xaxis.location)
}
if(!missing(yaxis.location)) {
yaxis.location <- tolower(yaxis.location)
if (yaxis.location %in% c('left', 'right'))
sideRow <- which(axis.locations == yaxis.location)
}
## Save the parameters for later API calls
##===========================================================
## For the updated API, we need to be able to access stuff passed into
## the original call to d3heatmap before everything is processed (and there
## is a lot of processing going on here). Primarily we need those items
## passed into the internal heatmap() function, which does the lion's share
## of the generating
params <- list(
x = x
, Rowv = Rowv
, Colv = Colv
, distfun = distfun
, hclustfun = hclustfun
, dendrogram = match.arg(dendrogram)
, reorderfun = reorderfun
, k_row = k_row
, k_col = k_col
, symm = symm
, revC = revC
, scale = match.arg(scale)
, scale.by.range = scale.by.range
, na.rm = na.rm
, na.value = na.value
, digits = digits
, cellnote = cellnote
, cellnote_scale = cellnote_scale
, labRow = labRow
, labCol = labCol
, col = col
, symbreaks = symbreaks
, na.color = na.color
, rng = rng
, breaks = breaks
, RowSideColors = RowSideColors
, ColSideColors = ColSideColors
, RowColorsPalette = RowColorsPalette
, ColColorsPalette = ColColorsPalette
)
## the big call to create the heatmap
##==============================
## inserting new call to the refactored heatmap function, which does everything up to
## this point that the old d3heatmap procedure did
hm <- do.call(heatmap, args = params)
x <- hm$x
## Colors for the heatmap and the color key (legend)
##===========================================
hm_colors <- heatmapColors(x
, params$col
, params$na.color
, params$na.rm
, params$rng
, params$scale
, params$breaks
, params$symbreaks
)
## axis and cellnote labels sync
##==============================
if (is.null(cellnote_row)) cellnote_row <- ylab
if (is.null(cellnote_col)) cellnote_col <- xlab
## font sizes
##==============================
if (is.null(cexCol)) cexCol <- 0.2 + 1 / log10(ncol(x))
if (is.null(cexRow)) cexRow <- 0.2 + 1 / log10(nrow(x))
## bundling the options
##==============================================
srtCol <- min(90, max(srtCol, 25))
key.location <- match.arg(key.location)
axis.locations <- c("top", "left", "bottom", "right")
if (!sideCol %in% c(1, 3)) sideCol <- 3
if (!sideRow %in% c(2, 4)) sideRow <- 4
options <- list(
hm_width = width
, hm_height = height
, xaxis_height = labColSize
, yaxis_width = labRowSize
, xaxis_font_size = cexCol * 12
, yaxis_font_size = cexRow * 12
, xaxis_angle = srtCol
, xaxis_location = axis.locations[sideCol]
, yaxis_location = axis.locations[sideRow]
, xaxis_title = xlab
, yaxis_title = ylab
, xaxis_title_font_size = xaxis_title_font_size
, yaxis_title_font_size = yaxis_title_font_size
, bins = hm_colors$breaks
, manual_breaks = (length(breaks) > 1)
, symbreaks = symbreaks
, print_values = print.values
, show_legend = key
, legend_scaler = as.numeric(keysize[1])
, legend_title = key.title
, legend_location = key.location
, legend_colors = hm_colors$legend_colors
, legend_bins = hm_colors$legend_bins
, legend_breaks = hm_colors$legend_breaks
, legend_type = match.arg(density.info)
, legend_fill = denscol
, brush_color = brush_color
, na_color = na.color
, show_grid = show_grid
, cellnote_row = cellnote_row
, cellnote_col = cellnote_col
, cellnote_val = cellnote_val
, cellnote_fontsize = notecex * 12
, cellnote_color = notecol
, anim_duration = anim_duration
, rsc_labs = hm$rsclabs
, csc_labs = hm$csclabs
, rsc_cols = hm$rsccols
, csc_cols = hm$csccols
, rsc_colnames = RowColorsNames
, csc_colnames = ColColorsNames
)
if (is.null(hm$rowDend)) c(options, list(yclust_width = 0))
if (is.null(hm$colDend)) c(options, list(xclust_height = 0))
# transpose will cause error if row colors is null
if (!is.null(hm$rowcolors)) hm$rowcolors <- t(hm$rowcolors)
## proceed to the widget
## NOTE: when loading the side colors, we transpose the
## rowSideColors
##=======================================
imgUri <- encodeAsPNG(t(x), hm_colors$col)
payload <- list(
rows = hm$rowDend
, cols = hm$colDend
, matrix = hm$mtx
, title = main
, image = imgUri
, rowcolors = hm$rowcolors
, colcolors = hm$colcolors
, theme = theme
, options = options
, params = params
)
# create widget
htmlwidgets::createWidget(
name = 'd3heatmap'
, payload # the x param
, width = width
, height = height
, package = 'd3heatmap'
, sizingPolicy = htmlwidgets::sizingPolicy(browser.fill = TRUE)
)
}
#' @import png base64enc
encodeAsPNG <- function(x, colors) {
colorData <- as.raw(col2rgb(colors(x), alpha = TRUE))
dim(colorData) <- c(4, ncol(x), nrow(x))
pngData <- png::writePNG(colorData)
encoded <- base64enc::base64encode(pngData)
paste0("data:image/png;base64,", encoded)
}
#' Wrapper functions for using d3heatmap in shiny
#'
#' Use \code{d3heatmapOutput} to create a UI element, and \code{renderD3heatmap}
#' to render the heatmap.
#'
#' @param outputId Output variable to read from
#' @param width,height The width and height of the map (see
#' \link[htmlwidgets]{shinyWidgetOutput})
#' @param expr An expression that generates a \code{\link{d3heatmap}} object
#' @param env The environment in which to evaluate \code{expr}
#' @param quoted Is \code{expr} a quoted expression (with \code{quote()})? This
#' is useful if you want to save an expression in a variable.
#'
#' @examples
#' \dontrun{
#' library(d3heatmap)
#' library(shiny)
#'
#' ui <- fluidPage(
#' h1("A heatmap demo"),
#' selectInput("palette", "Palette", c("YlOrRd", "RdYlBu", "Greens", "Blues")),
#' checkboxInput("cluster", "Apply clustering"),
#' d3heatmapOutput("heatmap")
#' )
#'
#' server <- function(input, output, session) {
#' output$heatmap <- renderD3heatmap({
#' d3heatmap(
#' scale(mtcars),
#' col = input$palette,
#' dendrogram = if (input$cluster) "both" else "none"
#' )
#' })
#' }
#'
#' shinyApp(ui, server)
#' }
#'
#' @export
d3heatmapOutput <- function(outputId, width = '100%', height = '400px'){
shinyWidgetOutput(outputId, 'd3heatmap', width, height, package = 'd3heatmap')
}
#' @rdname d3heatmapOutput
#' @export
renderD3heatmap <- function(expr, env = parent.frame(), quoted = FALSE) {
if (!quoted) { expr <- substitute(expr) } # force quoted
shinyRenderWidget(expr, d3heatmapOutput, env, quoted = TRUE)
}
rstudio/d3heatmap documentation built on Nov. 18, 2024, 9:20 a.m.
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Defines functions renderD3heatmap d3heatmapOutput encodeAsPNG d3heatmap
Documented in d3heatmap d3heatmapOutput renderD3heatmap
#' @import htmlwidgets
#' @importFrom grDevices col2rgb rgb colorRampPalette
#' @importFrom stats as.dendrogram dendrapply dist hclust is.leaf order.dendrogram reorder sd
#' @importFrom utils capture.output str
NULL
#' D3 Heatmap widget
#'
#' Creates a D3.js-based heatmap widget.
#'
#' @param x A numeric matrix or data.frame with numeric columns. All non-numeric columns
#' will be filtered out
#'
#' @param main \emph{string} Plot title. Defaults to \code{NULL}.
#'
#' @param theme A custom CSS theme to use. Currently the only valid values are
#' \code{""} and \code{"dark"}. \code{"dark"} is primarily intended for
#' standalone visualizations, not R Markdown or Shiny.
#'
#' @param col Either a colorbrewer2.org palette name (e.g. \code{"YlOrRd"}
#' or \code{"Blues"}), or a vector of colors to interpolate in hexadecimal
#' \code{"#RRGGBB"} format, or a color interpolation function like
#' \code{\link[grDevices]{colorRamp}}.
#'
#' @param breaks \emph{integer} Either a numeric vector indicating the splitting
#' points for binning x into colors, or a integer number of break points
#' to be used, in which case the break points will be spaced equally
#' between min(x) and max(x).
#'
#' @param symbreaks \emph{logical} Arrange color bins symmetrically around zero?
#'
#' @param Rowv determines if and how the row dendrogram
#' should be reordered. By default, it is TRUE, which implies
#' dendrogram is computed and reordered based on row means.
#' If NULL or FALSE, then no dendrogram is computed and no reordering
#' is done. If a dendrogram, then it is used "as-is", i.e. without any
#' reordering. If a vector of integers, then a dendrogram is computed
#' and reordered based on the order of the vector.
#'
#' @param Colv determines if and how the column dendrogram should be
#' reordered. Has the options as the Rowv argument above and additionally
#' when x is a square matrix, Colv = "Rowv" means that columns should be
#' treated identically to the rows.
#'
#' @param distfun function used to compute the distance (dissimilarity)
#' between both rows and columns. Defaults to dist.
#'
#' @param hclustfun function used to compute the hierarchical clustering
#' when Rowv or Colv are not dendrograms. Defaults to hclust.
#'
#' @param dendrogram character string indicating whether to draw 'none',
#' 'row', 'column' or 'both' dendrograms. Defaults to 'both'. However, if
#' Rowv (or Colv) is FALSE or NULL and dendrogram is 'both', then a warning
#' is issued and Rowv (or Colv) arguments are honored.
#'
#' @param reorderfun function(d, w) of dendrogram and weights for reordering
#' the row and column dendrograms. The default uses stats{reorder.dendrogram}
#'
#' @param k_row,kr an integer scalar with the desired number of groups by which
#' to color the dendrogram's branches in the rows
#' (uses \link[dendextend]{color_branches})
#'
#' @param k_col,kc an integer scalar with the desired number of groups by which
#' to color the dendrogram's branches in the columns
#' (uses \link[dendextend]{color_branches})
#'
#' @param print.values \emph{logical} Show the values inside the cells. Defaults to \code{FALSE}.
#'
#' @param key Show color key and density
#' information? \code{TRUE/FALSE}. Defaults to \code{FALSE}
#'
#' @param keysize \emph{numeric} value indicating the relative size of the key. Will multiple the labRowSize and labColSize.
#' Defaults to 1
#'
#' @param key.title Separate title for color key. Defaults to \code{NULL}.
#'
#' @param key.location \emph{Required, character} Location for color key, either \code{"fl", "br", "tr"
#' "tl", or "bl"} for "float", "bottom right", "top right", "top left", and "bottom left".
#' Defaults to \code{"fl"}, which follows the location of the axis labels.
#'
#' @param density.info \emph{Optional, character} indicating whether to superimpose
#' a 'histogram' or no plot ('none') on the color-key (legend).
#'
#' @param denscol \emph{Optional, character} giving the color for the density
#' display specified by 'density.info', defaults to \code{NULL} which will fill the
#' bars with the same color as the bin
#'
#' @param width Width in pixels (optional, defaults to automatic sizing).
#'
#' @param height Height in pixels (optional, defaults to automatic sizing).
#'
#' @param labColSize Size of axes, in pixels.
#'
#' @param labRowSize Size of axes, in pixels.
#'
#' @param cexCol Font size of column labels, as a scalar to '12px' font. Default to
#' 0.2 + 1/log10(ncol(x)).
#'
#' @param cexRow Font size of row labels, as a scalar to '12px' font size. Defaults to
#' 0.2 + 1/log10(nrow(x)).
#'
#' @param srtCol Angle of axis labels. Defaults to 60. Maximum of 90 (vertical), minimum of 25.
#'
#' @param sideCol,xaxis.location 3 or 1, for "bottom" or "top", which side column labels
#' display. Defaults to 3 ("bottom"). For \code{xaxis.location} use "bottom"
#' or "top".
#'
#' @param sideRow,yaxis.location 2 or 4, for "left" or "right", which side row labels
#' display. Defaults to 4 ("right"). For \code{yaxis.location} use "left" or "right".
#'
#' @param xlab Title text of x axis
#'
#' @param ylab Title text of y axis
#'
#' @param xaxis_title_font_size Font size of x axis title in pixels. Defaults to 14.
#'
#' @param yaxis_title_font_size Font size of y axis title in pixels. Defaults to 14.
#'
#' @param brush_color The base color to be used for the brush. The brush will be
#' filled with a low-opacity version of this color. \code{"#RRGGBB"} format
#' expected.
#'
#' @param show_grid \code{TRUE} to show gridlines, \code{FALSE} to hide them, or
#' a numeric value to specify the gridline thickness in pixels (can be a non-integer).
#'
#' @param anim_duration Number of milliseconds to animate zooming in and out.
#' For large \code{x} it may help performance to set this value to \code{0}.
#'
#' @param symm logical indicating if x should be treated symmetrically; can only be true when x is a square matrix.
#'
#' @param revC logical indicating if the column order should be reversed for plotting.
#' Default (when missing) - is FALSE, unless symm is TRUE.
#' This is useful for cor matrix.
#'
#' @param scale character indicating if the values should be centered and scaled in either
#' the row direction or the column direction, or none. The default is "none".
#'
#' @param scale.by.range logical indicating whether to scale rows or columns by
#' the range of each row and column. Setting this parameter to \code{TRUE}
#' automatically sets \code{na.rm} to \code{TRUE}
#'
#' @param na.rm logical indicating whether NA's should be removed.
#'
#' @param na.value numeric indicating where NA's should be substituted to trigger the NA color.
#'
#' @param na.color Color of NA values in heatmap. Defaults to neutral gray.
#'
#' @param rng A vector of two numbers, namely the minimum and maximum value
#' to use when determining the mapping from values to colors. This is useful
#' when the range of values changes between heatmaps, but colors should be the
#' same (optional, defaults to the minimum and maximum of \code{x}).
#'
#' @param digits \emph{integer} indicating the number of decimal places to be used by \link{round} for 'label'.
#'
#' @param notecol \emph{character} name or hex specifying the color of the values printed
#' inside the cells
#'
#' @param notecex,cex.note \emph{numeric} scalar of 12 to determine pixel size of printed cell values.
#' inside the cells. If not specified, the minimum font size between the x and y axes.
#'
#' @param cellnote_row \emph{character} Label to display next to the row value when the user hovers over the cell.
#' If not specified, tries to match the \code{xlab}; if no axis title, defaults to "Row".
#'
#' @param cellnote_col \emph{character} Label to display next to the column value when the user hovers over the cell.
#' If not specified, tries to match the \code{ylab}; if no axis title, defaults to "Col".
#'
#' @param cellnote_val \emph{character} Label to display next to the cell value when the user hovers over the cell.
#' Defaults to "Value".
#'
#' @param cellnote \emph{numeric} (optional) matrix of the same dimensions as \code{x} that has the human-readable version of each value, for displaying to the user on hover. If \code{NULL}, then \code{x} will be coerced using \code{\link{as.character}}.
#' If missing, it will use \code{x}, after rounding it based on the \code{digits} parameter.
#'
#' @param cellnote_scale \emph{logical} (default is FALSE). IF cellnote is missing and x is used, should cellnote be scaled if x is also scaled?
#'
#' @param labRow character vectors with row labels to use (from top to bottom); default to rownames(x).
#'
#' @param labCol character vectors with column labels to use (from left to right); default to colnames(x).
#'
#' @param ColSideColors (optional) character vector of length ncol(x), or matrix with
#' columns equal to ncol(x), containing the color names for a horizontal side bar that may
#' be used to annotate the columns of x. \code{ColIndividualColors}, from heatmap.2, can
#' also be used
#'
#' @param RowSideColors (optional) character vector of length nrow(x), or matrix with rows
#' equal to nrow(x), containing the color names for a vertical side bar that may be used to
#' annotate the rows of x. \code{RowIndividualColors}, from heatmap.3, can also be used
#'
#' @param RowColorsPalette a palette of colors to use for RowSideColors if passing a non-color matrix
#'
#' @param ColColorsPalette a palette of colors to use for ColSideColors if passing a non-color matrix
#'
#' @param RowColorsNames the names of the variables for RowSideColors. Overrides colnames(RowSideColors)
#'
#' @param ColColorsNames the names of the variables for ColSideColors. Overrides rownames(ColSideColors)
#' with rows equal to nrow(x), containing the color names for a vertical side bar that may be used to annotate the
#' rows of x.
#'
#' @param ... a catch for undocumented features or unused arguments from heatmap.2
#' or heatmap.3, to enable direct use of those formulations in d3heatmap
#'
#' @import htmlwidgets
#'
#' @source
#' The interface was designed based on \link{heatmap} and \link[gplots]{heatmap.2}
#'
#' @seealso
#' \link{heatmap}, \link[gplots]{heatmap.2}
#'
#' @examples
#' \dontrun{
#'
#' d3heatmap(mtcars, scale = "column", col = "Blues")
#'
#' }
#'
#' @export
d3heatmap <- function(x
, main = NULL
, width = NULL
, height = NULL
, show_grid = TRUE
, anim_duration = 500
, rng = NULL
## dendrogram control
, symm = FALSE
, Rowv = TRUE
, Colv = if (symm) "Rowv" else TRUE
, distfun = dist
, hclustfun = hclust
, dendrogram = c("both", "row", "column", "none")
, reorderfun = function(d, w) reorder(d, w)
, k_row = NULL
, k_col = NULL
, kr
, kc
, revC = NULL
## data scaling
, scale = c("none", "row", "column")
, scale.by.range = FALSE
, na.rm = TRUE
, na.color = "#777777"
, na.value = NA
## legend (color key)
, key = FALSE
, keysize = 1
, key.title = NULL
, key.location = c("fl", "br", "tr", "tl", "bl")
, density.info = c('histogram', 'none')
, denscol = NULL
## cellnote formatting
, digits = 3L
, cellnote = NULL
, cellnote_scale = FALSE
, cellnote_row = NULL
, cellnote_col = NULL
, cellnote_val = "Value"
, brush_color = "#0000FF"
, print.values = FALSE
, notecol = '#222222'
, notecex = 1
, cex.note
## color controls
, theme = NULL
, col = "RdYlBu"
, breaks = NULL
, symbreaks = FALSE
## axis controls
, labRow = rownames(x)
, labCol = colnames(x)
, labColSize = 80
, labRowSize = 120
, cexCol = NULL
, cexRow = NULL
, srtCol = 60
, sideCol = 3
, sideRow = 4
, xaxis.location
, yaxis.location
, xlab = NULL
, ylab = NULL
, xaxis_title_font_size = 14
, yaxis_title_font_size = 14
# side colors
, ColSideColors = NULL
, RowSideColors = NULL
, RowColorsPalette = NULL
, ColColorsPalette = NULL
, RowColorsNames = NULL
, ColColorsNames = NULL
, ...
) {
if(length(dim(x)) != 2) {
stop(paste("x is not a 2-dimensional object. Here is the str output of x:", capture.output(str(x)), collapse = "\n"))
}
if(is.matrix(x) && !is.numeric(x)) {
warning(paste(capture.output(str(x)), collapse = "\n"))
stop("d3heatmap data must be a numeric
matrix or a data.frame with numeric columns")
}
# we'll modify this to take any matrix or data.frame, but filter out all
# non-numeric columns
if (is.data.frame(x) | is.table(x))
x <- x[, sapply(x, is.numeric)]
opts <- list(...)
axis.locations <- c("top", "left", "bottom", "right")
## pre-process paraemters
##===========================================================
## process the overlap of parameters between the old d3heatmap,
## heatmap.2, and heatmap.3 APIs
if (!missing(kr)) k_row <- kr
if (!missing(kc)) k_col <- kc
if (!missing(cex.note)) notecex <- cex.note
if(!is.null(ColSideColors))
ColSideColors <- matrix(ColSideColors, ncol = ncol(x))
if(!is.null(RowSideColors))
RowSideColors <- matrix(RowSideColors, nrow = nrow(x))
if (!is.null(opts$ColIndividualColors))
ColSideColors <- matrix(opts$ColIndividualColors, ncol = ncol(x))
if (!is.null(opts$RowIndividualColors))
RowSideColors <- matrix(opts$RowIndividualColors, nrow = nrow(x))
if (is.null(RowColorsPalette))
RowColorsPalette <- c('blue', 'orange', 'black')
if (is.null(ColColorsPalette))
ColColorsPalette <- c('cyan', 'maroon', 'grey')
if (is.null(RowColorsNames)) RowColorsNames <- colnames(RowSideColors)
if (is.null(ColColorsNames)) ColColorsNames <- rownames(ColSideColors)
## additional controls for working with the gadget (shiny inputs)
##===========================================================
if (!is.null(k_row)) if (is.na(k_row)) k_row <- NULL
if (!is.null(k_col)) if (is.na(k_col)) k_col <- NULL
if (!is.null(cexCol)) if (is.na(cexCol)) cexCol <- NULL
if (!is.null(cexRow)) if (is.na(cexRow)) cexRow <- NULL
if(!missing(xaxis.location)) {
xaxis.location <- tolower(xaxis.location)
if (xaxis.location %in% c('top', 'bottom'))
sideCol <- which(axis.locations == xaxis.location)
}
if(!missing(yaxis.location)) {
yaxis.location <- tolower(yaxis.location)
if (yaxis.location %in% c('left', 'right'))
sideRow <- which(axis.locations == yaxis.location)
}
## Save the parameters for later API calls
##===========================================================
## For the updated API, we need to be able to access stuff passed into
## the original call to d3heatmap before everything is processed (and there
## is a lot of processing going on here). Primarily we need those items
## passed into the internal heatmap() function, which does the lion's share
## of the generating
params <- list(
x = x
, Rowv = Rowv
, Colv = Colv
, distfun = distfun
, hclustfun = hclustfun
, dendrogram = match.arg(dendrogram)
, reorderfun = reorderfun
, k_row = k_row
, k_col = k_col
, symm = symm
, revC = revC
, scale = match.arg(scale)
, scale.by.range = scale.by.range
, na.rm = na.rm
, na.value = na.value
, digits = digits
, cellnote = cellnote
, cellnote_scale = cellnote_scale
, labRow = labRow
, labCol = labCol
, col = col
, symbreaks = symbreaks
, na.color = na.color
, rng = rng
, breaks = breaks
, RowSideColors = RowSideColors
, ColSideColors = ColSideColors
, RowColorsPalette = RowColorsPalette
, ColColorsPalette = ColColorsPalette
)
## the big call to create the heatmap
##==============================
## inserting new call to the refactored heatmap function, which does everything up to
## this point that the old d3heatmap procedure did
hm <- do.call(heatmap, args = params)
x <- hm$x
## Colors for the heatmap and the color key (legend)
##===========================================
hm_colors <- heatmapColors(x
, params$col
, params$na.color
, params$na.rm
, params$rng
, params$scale
, params$breaks
, params$symbreaks
)
## axis and cellnote labels sync
##==============================
if (is.null(cellnote_row)) cellnote_row <- ylab
if (is.null(cellnote_col)) cellnote_col <- xlab
## font sizes
##==============================
if (is.null(cexCol)) cexCol <- 0.2 + 1 / log10(ncol(x))
if (is.null(cexRow)) cexRow <- 0.2 + 1 / log10(nrow(x))
## bundling the options
##==============================================
srtCol <- min(90, max(srtCol, 25))
key.location <- match.arg(key.location)
axis.locations <- c("top", "left", "bottom", "right")
if (!sideCol %in% c(1, 3)) sideCol <- 3
if (!sideRow %in% c(2, 4)) sideRow <- 4
options <- list(
hm_width = width
, hm_height = height
, xaxis_height = labColSize
, yaxis_width = labRowSize
, xaxis_font_size = cexCol * 12
, yaxis_font_size = cexRow * 12
, xaxis_angle = srtCol
, xaxis_location = axis.locations[sideCol]
, yaxis_location = axis.locations[sideRow]
, xaxis_title = xlab
, yaxis_title = ylab
, xaxis_title_font_size = xaxis_title_font_size
, yaxis_title_font_size = yaxis_title_font_size
, bins = hm_colors$breaks
, manual_breaks = (length(breaks) > 1)
, symbreaks = symbreaks
, print_values = print.values
, show_legend = key
, legend_scaler = as.numeric(keysize[1])
, legend_title = key.title
, legend_location = key.location
, legend_colors = hm_colors$legend_colors
, legend_bins = hm_colors$legend_bins
, legend_breaks = hm_colors$legend_breaks
, legend_type = match.arg(density.info)
, legend_fill = denscol
, brush_color = brush_color
, na_color = na.color
, show_grid = show_grid
, cellnote_row = cellnote_row
, cellnote_col = cellnote_col
, cellnote_val = cellnote_val
, cellnote_fontsize = notecex * 12
, cellnote_color = notecol
, anim_duration = anim_duration
, rsc_labs = hm$rsclabs
, csc_labs = hm$csclabs
, rsc_cols = hm$rsccols
, csc_cols = hm$csccols
, rsc_colnames = RowColorsNames
, csc_colnames = ColColorsNames
)
if (is.null(hm$rowDend)) c(options, list(yclust_width = 0))
if (is.null(hm$colDend)) c(options, list(xclust_height = 0))
# transpose will cause error if row colors is null
if (!is.null(hm$rowcolors)) hm$rowcolors <- t(hm$rowcolors)
## proceed to the widget
## NOTE: when loading the side colors, we transpose the
## rowSideColors
##=======================================
imgUri <- encodeAsPNG(t(x), hm_colors$col)
payload <- list(
rows = hm$rowDend
, cols = hm$colDend
, matrix = hm$mtx
, title = main
, image = imgUri
, rowcolors = hm$rowcolors
, colcolors = hm$colcolors
, theme = theme
, options = options
, params = params
)
# create widget
htmlwidgets::createWidget(
name = 'd3heatmap'
, payload # the x param
, width = width
, height = height
, package = 'd3heatmap'
, sizingPolicy = htmlwidgets::sizingPolicy(browser.fill = TRUE)
)
}
#' @import png base64enc
encodeAsPNG <- function(x, colors) {
colorData <- as.raw(col2rgb(colors(x), alpha = TRUE))
dim(colorData) <- c(4, ncol(x), nrow(x))
pngData <- png::writePNG(colorData)
encoded <- base64enc::base64encode(pngData)
paste0("data:image/png;base64,", encoded)
}
#' Wrapper functions for using d3heatmap in shiny
#'
#' Use \code{d3heatmapOutput} to create a UI element, and \code{renderD3heatmap}
#' to render the heatmap.
#'
#' @param outputId Output variable to read from
#' @param width,height The width and height of the map (see
#' \link[htmlwidgets]{shinyWidgetOutput})
#' @param expr An expression that generates a \code{\link{d3heatmap}} object
#' @param env The environment in which to evaluate \code{expr}
#' @param quoted Is \code{expr} a quoted expression (with \code{quote()})? This
#' is useful if you want to save an expression in a variable.
#'
#' @examples
#' \dontrun{
#' library(d3heatmap)
#' library(shiny)
#'
#' ui <- fluidPage(
#' h1("A heatmap demo"),
#' selectInput("palette", "Palette", c("YlOrRd", "RdYlBu", "Greens", "Blues")),
#' checkboxInput("cluster", "Apply clustering"),
#' d3heatmapOutput("heatmap")
#' )
#'
#' server <- function(input, output, session) {
#' output$heatmap <- renderD3heatmap({
#' d3heatmap(
#' scale(mtcars),
#' col = input$palette,
#' dendrogram = if (input$cluster) "both" else "none"
#' )
#' })
#' }
#'
#' shinyApp(ui, server)
#' }
#'
#' @export
d3heatmapOutput <- function(outputId, width = '100%', height = '400px'){
shinyWidgetOutput(outputId, 'd3heatmap', width, height, package = 'd3heatmap')
}
#' @rdname d3heatmapOutput
#' @export
renderD3heatmap <- function(expr, env = parent.frame(), quoted = FALSE) {
if (!quoted) { expr <- substitute(expr) } # force quoted
shinyRenderWidget(expr, d3heatmapOutput, env, quoted = TRUE)
}
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