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

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

Description

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

Usage

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

## 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)

Example output

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: dnet
Loading required package: supraHex
Loading required package: hexbin
Loading required package: ggplot2
data.main: 32 rows X 6 columns
data.meta: 32 rows X 5 columns (5 continuous + 0 discrete)
widths: 0.40 (meta), 0.20 (blank), 2.40 (legend)
data.main: 32 rows X 6 columns
data.meta: 32 rows X 5 columns (5 continuous + 0 discrete)
widths: 0.40 (meta), 0.20 (blank), 4.00 (legend)

XGR documentation built on Jan. 8, 2020, 5:06 p.m.