xHeatmapAdv: Function to draw heatmap together with sidebars on rows using...

Description Usage Arguments Value Note See Also Examples

View source: R/xHeatmapAdv.r

Description

xHeatmapAdv is supposed to draw heatmap together with sidebars on rows using ggplot2.

Usage

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xHeatmapAdv(data.main, data.meta, reorder = c("none", "row", "col",
"both"), colormap = "spectral", ncolors = 64, zlim = NULL,
barwidth = 0.3, barheight = 4, nbin = 64, legend.title = "Main",
x.rotate = 60, x.text.size = 6, x.text.hjust = 0.5,
y.text.size = 6, legend.text.size = 5, 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 = "grey80",
data.label = NULL, label.size = 1, label.color = "black",
meta.colormap = "spectral", meta.x.rotate = 75,
meta.shape.continuous = 15, meta.shape.discrete = 95,
meta.size = 2, meta.location = c("right", "left"),
meta.width = 0.5, gap.width = 0.5, legend.width = NULL,
legend.direction = c("vertical", "horizontal"), legend.nrow = NULL,
verbose = TRUE, ...)

Arguments

data.main

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

data.meta

a data frame/matrix for metadata visualisation. The per-column coloring can be continuous (numeric) or discrete (factor)

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 'grey80'

data.label

a data frame/matrix used for the labelling

label.size

the label size

label.color

the label color

meta.colormap

the colormap for metadata

meta.x.rotate

the angle to rotate the x tick labelings for the metadata. By default, it is 90

meta.shape.continuous

the number specifying the shape for continuous metadata. By default, it is 15

meta.shape.discrete

the number specifying the shape for discrete metadata. By default, it is 95

meta.size

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

meta.location

the location of metadata. It can be "right" or "left"

meta.width

the width for each column in metadata. By default, it is 0.5 (relative to each column in main data)

gap.width

the width for the gap between panels. By default, it is 0.5 (relative to each column in main data)

legend.width

the width for the legend. By default, it is NULL automatically determined (which can be used as a reference to define later for the better visualisation)

legend.direction

the direction of the legend. It can be "vertical" or "horizontal"

legend.nrow

the row number for legends. By default, it is 3 for the vertical direction of the legend; 6 for the horizontal direction of the legend

verbose

logical to indicate whether the messages will be displayed in the screen. By default, it sets to true for display

...

additional graphic parameters for supraHex::visTreeBootstrap

Value

a gtable object

Note

none

See Also

xHeatmap

Examples

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## Not run: 
# Load the XGR package
library(XGR)
data(mtcars)
data.main <- mtcars[,1:6]
data.meta <- mtcars[,7:11]
gt <- xHeatmapAdv(data.main, data.meta, barwidth=0.3, barheight=2.5,
meta.location="right", legend.nrow=3, meta.width=0.4, gap.width=0.2,
legend.width=NULL)
gt <- xHeatmapAdv(data.main, data.meta, barwidth=0.3, barheight=4,
meta.location="right", legend.nrow=6, meta.width=0.4, gap.width=0.2,
legend.width=4)
dev.new(); grid::grid.draw(gt)

## End(Not run)

hfang-bristol/XGR documentation built on Dec. 12, 2018, 1:29 p.m.