plot.stat: Plot the fourthcorner analysis for transcriptomic data
In covRNA: Multivariate Analysis of Transcriptomic Data

Description Usage Arguments Value Author(s) Examples

View source: R/plot.stat.R

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).

## 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, ...)

`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.