XGR (version 1.1.5)

xHeatmap: Function to draw heatmap using ggplot2

Description

xHeatmap is supposed to draw heatmap using ggplot2.

Usage

xHeatmap(data, reorder = c("none", "row", "col", "both"),
colormap = "spectral", ncolors = 64, zlim = NULL, barwidth = 0.3,
barheight = NULL, nbin = 64, legend.title = "", x.rotate = 90,
x.text.size = 6, x.text.hjust = 0, y.text.size = 6,
legend.text.size = 4, legend.title.size = 6, shape = 19,
size = 2, plot.margin = unit(c(5.5, 5.5, 5.5, 5.5), "pt"),
font.family = "sans", na.color = "transparent", data.label = NULL,
label.size = 1, label.color = "black", ...)

Arguments

data

a data frame/matrix for coloring. The coloring can be continuous (numeric matrix) or discrete (factor matrix)

reorder

how to reorder rows and columns. It can be "none" for no reordering, "row" for reordering rows according to number of sharings (by default), "col" for reordering columns, and "both" for reordering rows and columns

colormap

short name for the colormap. It can be one of "jet" (jet colormap), "bwr" (blue-white-red colormap), "gbr" (green-black-red colormap), "wyr" (white-yellow-red colormap), "br" (black-red colormap), "yr" (yellow-red colormap), "wb" (white-black colormap), and "rainbow" (rainbow colormap, that is, red-yellow-green-cyan-blue-magenta). Alternatively, any hyphen-separated HTML color names, e.g. "blue-black-yellow", "royalblue-white-sandybrown", "darkgreen-white-darkviolet". A list of standard color names can be found in http://html-color-codes.info/color-names

ncolors

the number of colors specified over the colormap

zlim

the minimum and maximum z values for which colors should be plotted, defaulting to the range of the finite values of displayed matrix

barwidth

the width of the colorbar. Default value is 'legend.key.width' or 'legend.key.size' in 'theme' or theme

barheight

the height of the colorbar. Default value is 'legend.key.height' or 'legend.key.size' in 'theme' or theme

nbin

the number of bins for drawing colorbar

legend.title

the title of the colorbar. By default, it is ''

x.rotate

the angle to rotate the x tick labelings. By default, it is 60

x.text.size

the text size of the x tick labelings. By default, it is 6

x.text.hjust

the hjust of the x tick labelings. By default, it is 0.5

y.text.size

the text size of the y tick labelings. By default, it is 6

legend.text.size

the text size of the legend tick labelings. By default, it is 5

legend.title.size

the text size of the legend titles. By default, it is 6

shape

the number specifying the shape. By default, it is 19

size

the number specifying the shape size. By default, it is 2

plot.margin

the margin (t, r, b, l) around plot. By default, it is unit(c(5.5,5.5,5.5,5.5),"pt")

font.family

the font family for texts

na.color

the color for NAs. By default, it is 'transparent'

data.label

a data frame/matrix used for the labelling

label.size

the label size

label.color

the label color

...

additional graphic parameters for supraHex::visTreeBootstrap

Value

a ggplot2 object

See Also

xHeatmap

Examples

# NOT RUN {
# Load the XGR package and specify the location of built-in data
library(XGR)
data(mtcars)
gp <- xHeatmap(mtcars, reorder="none", colormap='jet.top', x.rotate=45,
shape=19, size=3, x.text.size=8,y.text.size=8, legend.title='mtcars')
gp + theme(legend.position="bottom",legend.direction="horizontal") +
guides(color=guide_colorbar(title="mtcars",title.position="top",barwidth=5,barheight=0.3))
gp + theme(legend.position="bottom",legend.direction="horizontal") +
guides(color=guide_legend(title="mtcars",title.position="top",barwidth=5,barheight=0.3))
gp + geom_text(aes(x, y,
label=val),size=1.8,color='black',fontface='bold',na.rm=TRUE,angle=45)
# }