GOHeat: Displays heatmap of the relationship between genes and terms.

In GOplot: Visualization of Functional Analysis Data

Description

The GOHeat function generates a heatmap of the relationship between genes and terms. Biological processes are displayed in rows and genes in columns. In addition genes are clustered to highlight groups of genes with similar annotated functions. The input can be generated with the chord_dat function.

Usage

GOHeat(data, nlfc, fill.col)

Arguments

data	The matrix represents the binary relation (1= is related to, 0= is not related to) between a set of genes (rows) and processes (columns)
nlfc	Defines the number of logFC columns (default = 0)
fill.col	Defines the color scale break points

Details

The heatmap has in general two modes which depend on the nlfc argument. If nlfc = 0, so no logFC values are available, the coloring encodes for the overall number of processes the respective gene is assigned to. In case of nlfc = 1 the color corresponds to the logFC of the gene.

Examples

## Not run: 
# Load the included dataset
data(EC)

# Generate the circ object
circ <- circle_dat(EC$david, EC$genelist)

# Generate the chord object
chord <- chord_dat(circ, EC$genes, EC$process)

# Create the plot with user-defined colors
GOHeat(chord, nlfc = 1, fill.col = c('red', 'yellow', 'green'))

## End(Not run)

Example output

Loading required package: ggplot2
Loading required package: ggdendro
Loading required package: gridExtra
Loading required package: RColorBrewer

GOplot documentation built on May 2, 2019, 8:57 a.m.