quheatmap: Visualization of identified biclusters

In QUBIC: An R package for qualitative biclustering in support of gene co-expression analyses

Description

This function can visualize the identifed biclusters using heatmap in support of overall expression pattern analysis,either for a single bicluster or two biclusters.

Usage

quheatmap(x, bicResult, number = 1, showlabel = FALSE, col = c("#313695",
  "#4575B4", "#74ADD1", "#ABD9E9", "#E0F3F8", "#FFFFBF", "#FEE090", "#FDAE61",
  "#F46D43", "#D73027", "#A50026"), ...)

Arguments

x	The data matrix
bicResult	biclust::BiclustResult object
number	which bicluster to be plotted
showlabel	If TRUE, show the xlabel and ylabel
col	default: c("#313695", "#4575B4", "#74ADD1", "#ABD9E9", "#E0F3F8", "#FFFFBF", "#FEE090", "#FDAE61", "#F46D43", "#D73027", "#A50026")
...	Additional options in fields::image.plot

See Also

qunet2xml QUBIC heatmapBC

Examples

# Load microarray matrix
data(BicatYeast)
res <- biclust::biclust(BicatYeast, method=BCQU(), verbose = FALSE)
# Draw heatmap for the 2th identified bicluster
par(mar = c(5, 4, 3, 5) + 0.1, mgp = c(0, 1, 0), cex.lab = 1.1, cex.axis = 0.5, cex.main = 1.1)
quheatmap(x = BicatYeast, res, number = 2, showlabel = TRUE)
# Draw heatmap for the 2th and 3th identified biclusters.
par(mar = c(5, 5, 5, 5), cex.lab = 1.1, cex.axis = 0.5, cex.main = 1.1)
quheatmap(x = BicatYeast, res, number = c(2, 3), showlabel = TRUE)

Example output

Loading required package: biclust
Loading required package: MASS
Loading required package: grid
Loading required package: colorspace
Loading required package: lattice
Loading required namespace: fields
[1] "yto 0"
[1] "xlo 0"

QUBIC documentation built on Nov. 8, 2020, 8:17 p.m.