heatmaply (version 0.7.1)

heatmaply: Cluster heatmap based on plotly

Description

An object of class heatmapr includes all the needed information for producing a heatmap. The goal is to seperate the pre-processing of the heatmap elements from the graphical rendaring of the object, which could be done

(Please submit an issue on github if you have a feature that you wish to have added)

Usage

heatmaply(x, colors = viridis(n = 256, alpha = 1, begin = 0, end = 1, option = "viridis"), limits = NULL, na.value = "grey50", row_text_angle = 0, column_text_angle = 45, subplot_margin = 0, dendrogram = "both", row_dend_left = FALSE, margins = c(50, 50, NA, 0), ..., scale_fill_gradient_fun = scale_fill_gradientn(colors = if (is.function(colors)) colors(256) else colors, na.value = na.value, limits = limits), grid_color = NA, srtRow, srtCol, xlab = "", ylab = "", main = "", titleX = TRUE, titleY = TRUE, hide_colorbar = FALSE, key.title = NULL, return_ppxpy = FALSE, row_side_colors = NULL, row_side_palette, col_side_colors = NULL, col_side_palette, ColSideColors = NULL, RowSideColors = NULL, heatmap_layers, branches_lwd = 0.6)

Arguments

x

can either be a heatmapr object, or a numeric matrix Defaults to TRUE unless x contains any NAs.

colors

a vector of colors to use for heatmap color. The default uses viridis(n=256, alpha = 1, begin = 0, end = 1, option = "viridis") It is passed to scale_fill_gradientn. If colors is a color function (with the first argument being `n` = the number of colors), it will be used to create 256 colors from that function.

limits

a two dimensional numeric vector specifying the data range for the scale.

na.value

color to use for missing values (default is "grey50").

row_text_angle

numeric (Default is 0), the angle of the text of the rows. (this is called srtRow in heatmap.2)

column_text_angle

numeric (Default is 45), the angle of the text of the columns. (this is called srtCol in heatmap.2)

subplot_margin

Currently not well implemented. It is passed to subplot. Default is 0. Either a single value or four values (all between 0 and 1). If four values are provided, the first is used as the left margin, the second is used as the right margin, the third is used as the top margin, and the fourth is used as the bottom margin. If a single value is provided, it will be used as all four margins.

dendrogram

Passed to heatmapr; "row", "column", or "both". Default is "both"

row_dend_left

logical (default is FALSE). Should the row dendrogram be plotted on the left side of the heatmap. If false then it will be plotted on the right side.

margins

numeric vector of length 4 (default is c(50,50,NA,0)) containing the margins (see layout) for column, row and main title names, respectively. The top margin is NA by default. If main=="" then the top margin will be set to 0, otherwise it will get 30. For a multiline title a larger default for the 3rd element should be set.

...

other parameters passed to heatmapr (currently, various parameters may be ignored.

scale_fill_gradient_fun

A function that creates a smooth gradient for the heatmap. The default uses scale_fill_gradientn with the values of colors, limits, and na.value that are supplied by the user. The user can input a customized function, such as scale_color_gradient() in order to get other results (although the virids default is quite recommended)

grid_color

control the color of the heatmap grid. Default is NA. Value passed to geom_tile. Do not use this parameter on larger matrix sizes, as it can dramatically prolong the build time of the heatmap. (another parameter, grid_color, will be added in the future - once it is implemented in plotly)

srtRow

if supplied, this overrides row_text_angle (this is to stay compatible with heatmap.2)

srtCol

if supplied, this overrides column_text_angle (this is to stay compatible with heatmap.2)

xlab

A character title for the x axis.

ylab

A character title for the y axis.

main

A character title for the heatmap.

titleX

logical (TRUE). should x-axis titles be retained? (passed to subplot).

titleY

logical (TRUE). should y-axis titles be retained? (passed to subplot).

hide_colorbar

logical (FALSE). If TRUE, then the color bar is hidden.

key.title

(character) main title of the color key. If set to NULL (default) no title will be plotted.

return_ppxpy

logical (FALSE). If TRUE, then no plotting is done and the p, px and py objects are returned (before turning into plotly objects). This is a temporary option which might be removed in the future just to make it easy to create a ggplot heatmaps.

row_side_colors, col_side_colors

data.frame of factors to produce row/column side colors in the style of heatmap.2/heatmap.3. col_side_colors should be "wide", ie be the same dimensions as the column side colors it will produce.

row_side_palette, col_side_palette

Color palette functions to be used for row_side_colors and col_side_colors respectively.

ColSideColors, RowSideColors

passed to row_side_colors,col_side_colors in order to keep compatibility with heatmap.2

heatmap_layers

ggplot object (eg, theme_bw()) to be added to the heatmap before conversion to a plotly object.

branches_lwd

numeric (default is 0.6). The width of the dendrograms' branches. If NULL then it is ignored. If the "lwd" is already defined in Rowv/Colv then this parameter is ignored (it is checked using has_edgePar("lwd")).

Examples

## Not run: 
# 
# # mtcars
# # x <- heatmapr(mtcars)
# library(heatmaply)
# heatmaply(iris[,-5], k_row = 3, k_col = 2)
# heatmaply(cor(iris[,-5]))
# heatmaply(cor(iris[,-5]), limits = c(-1,1))
# heatmaply(mtcars, k_row = 3, k_col = 2)
# 
# # make sure there is enough room for the labels:
# heatmaply(mtcars, margins = c(40, 130))
# # this is the same as using:
# heatmaply(mtcars) %>% layout(margin = list(l = 130, b = 40))
# 
# # control text angle
# heatmaply(mtcars, column_text_angle = 90, margins = c(40, 130))
# # the same as using srtCol:
# # heatmaply(mtcars, srtCol = 90) %>% layout(margin = list(l = 130, b = 40))
# 
# 
# 
# x <- mtcars
# # different colors
# heatmaply(x, colors = heat.colors(200))
# # using special scale_fill_gradient_fun colors
# heatmaply(x, scale_fill_gradient_fun = scale_color_gradient())
# 
# 
# # We can join two heatmaps together:
# library(heatmaply)
# hm1 <- heatmaply(mtcars, margins = c(40, 130))
# hm2 <- heatmaply(mtcars, scale = "col", margins = c(40, 130))
# subplot(hm1, hm2, margin = .2)
# 
# # If we want to share the Y axis, then it is risky to keep any of the dendrograms:
# library(heatmaply)
# hm1 <- heatmaply(mtcars, Colv = FALSE, Rowv = FALSE, margins = c(40, 130))
# hm2 <- heatmaply(mtcars, scale = "col" , Colv = FALSE, Rowv = FALSE,
#              margins = c(40, 130))
# subplot(hm1, hm2, margin = .02, shareY = TRUE)
# 
# # We can save heatmaply as a widget by using:
# library(heatmaply)
# library(htmlwidgets)
# heatmaply(iris[,-5]) %>%
#    saveWidget(file="test.html",selfcontained = FALSE)
# 
# 
# # Example for using RowSideColors
# 
# x  <- as.matrix(datasets::mtcars)
# rc <- colorspace::rainbow_hcl(nrow(x))
# 
# library(gplots)
# library(viridis)
# heatmap.2(x, trace = "none", col = viridis(100),
#           RowSideColors=rc)
# 
# heatmaply(x, seriate = "mean",
#           RowSideColors=rc)
# 
# 
# heatmaply(x[,-c(8,9)], seriate = "mean",
#           col_side_colors = c(rep(0,5), rep(1,4)),
#           row_side_colors = x[,8:9])
# heatmaply(x[,-c(8,9)], seriate = "mean",
#           col_side_colors = data.frame(a=c(rep(0,5), rep(1,4))),
#           row_side_colors = x[,8:9])
# 
# 
# 
# ## End(Not run)