GOCircle: Circular visualization of the results of a functional...

In GOplot: Visualization of Functional Analysis Data

Description

The circular plot combines gene expression and gene- annotation enrichment data. A subset of terms is displayed like the GOBar plot in combination with a scatterplot of the gene expression data. The whole plot is drawn on a specific coordinate system to achieve the circular layout.The segments are labeled with the term ID.

Usage

GOCircle(data, title, nsub, rad1, rad2, table.legend = T, zsc.col, lfc.col,
  label.size, label.fontface)

Arguments

data	A special data frame which should be the result of circle_dat
title	The title of the plot
nsub	A numeric or character vector. If it's numeric then the number defines how many processes are displayed (starting from the first row of data). If it's a character string of processes then these processes are displayed
rad1	The radius of the inner circle (default=2)
rad2	The radius of the outer circle (default=3)
table.legend	Shall a table be displayd or not? (default=TRUE)
zsc.col	Character vector to define the colour scale for the z-score of the form c(high, midpoint,low)
lfc.col	A character vector specifying the colour for up- and down-regulated genes
label.size	Size of the segment labels (default=5)
label.fontface	Font style of the segment labels (default='bold')

Details

The outer circle shows a scatter plot for each term of the logFC of the assigned genes. The colours can be changed with the argument lfc.col.

The nsub argument needs a bit more explanation to be used wisely. First of all, it can be a numeric or a character vector. If it is a character vector then it contains the IDs or term descriptions of the displayed processes.If nsub is a numeric vector then the number defines how many terms are displayed. It starts with the first row of the input data frame.

See Also

circle_dat, GOBar

Examples

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

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

# Creating the circular plot
GOCircle(circ)

# Creating the circular plot with a different colour scale for the logFC
GOCircle(circ, lfc.col = c('purple', 'orange'))

# Creating the circular plot with a different colour scale for the z-score
GOCircle(circ, zsc.col = c('yellow', 'black', 'cyan'))

# Creating the circular plot with different font style
GOCircle(circ, label.size = 5, label.fontface = 'italic')

## 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.