xHeatmap: Function to draw heatmap using ggplot2

In XGR: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis

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

Note

none

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)

## End(Not run)

XGR documentation built on June 18, 2019, 3:01 p.m.