plot.stat: Plot the fourthcorner analysis for transcriptomic data

Description Usage Arguments Value Author(s) Examples

View source: R/plot.stat.R

Description

The function plot produces a cross table of the gene and sample covariates of a stat object. Colours indicate positive/negative significance or absence of significance of the assciations (per default: white for non-significant, red for negative significant and red for positive significant associations).

Usage

1
2
3
4
## S3 method for class 'stat'
plot(x, col=c("lightgrey","deepskyblue","red"), sig=TRUE,
                    alpha=0.05, show=c("adj","non-adj"), cex=1, 
                    ynames, xnames, ytext=1, xtext=1, shiftx=0, shifty=0, ...)

Arguments

x

An object of class stat that shall be visualised as a cross table.

col

A vector of three colours. The first colour represents non-significant, the second positive significant, the third negative significant associations in the cross table.

sig

If TRUE (default), only covariates involved in at least one significant association are plotted.

alpha

The significance level.

show

'adj' or 'non-adj' indicate if adjusted or raw p-values shall be plotted, respectively.

cex

The magnitude of the text in the cross table.

ynames, xnames

Row and column names of the cross table. By default, the column names of R and Q are used, respectively.

ytext, xtext

Rotation of the row and column names of the cross table.

shifty, shiftx

Shift of the row and column names to the right or to the left.

...

More plotting parameters can be added.

Value

Plot of fourthcorner analysis.

Author(s)

Lara Urban

Examples

1
2
statBaca <- stat(Baca, nrcor = 2)
plot(statBaca)

covRNA documentation built on May 31, 2017, 10:56 a.m.