GOCircle {GOplot}

Circular visualization of the results of a functional analysis.

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)