showPair {EBcoexpress} | R Documentation |
This function plots the expression data for a given pair, coloring by condition. A regression line may be added; this line may be made robust so that it only uses those data points used by biweight midcorrelation
showPair(pair, X, conditions, gsep = "~", regLine = TRUE, useBWMC = TRUE, colors = NULL, ...)
pair |
A pair name, such as ABC~XYZ, where ~ is the separator given by gsep |
X |
An m-by-n expression matrix, where rows are genes and columns are chips (subjects); include all chips in X, indicate condition in the conditions array |
conditions |
The conditions array |
gsep |
A separator that indicates a gene-pair, such as P53~MAPK1. The separator should not appear in any of the gene names |
regLine |
Should a regression line be drawn for each condition? |
useBWMC |
Should the regression line be robust, a la biweight midcorrelation? |
colors |
Colors for the different conditions. Defaults to palette() |
... |
Other options to be passed to plot(), with three exceptions. The lty= and lwd= options will be passed to abline() and will have an effect on the plot when regLine=TRUE; col= is overwritten by the colors= array and may not be specified. All other ... options will be passed to the main plot. |
Returns invisble(NULL)
John A. Dawson <jadawson@wisc.edu>
Dawson JA and Kendziorski C. An empirical Bayesian approach for identifying differential co-expression in high-throughput experiments. (2011) Biometrics. E-publication before print: http://onlinelibrary.wiley.com/doi/10.1111/j.1541-0420.2011.01688.x/abstract
data(fiftyGenes) tinyCond <- c(rep(1,100),rep(2,25)) showPair("X1~X2",fiftyGenes, conditions=tinyCond, pch=20, xlim=c(-4,4), ylim=c(-4,4)) # showPair("X26~X35",fiftyGenes, conditions=tinyCond, pch=20, xlim=c(-4,4), ylim=c(-4,4)) # showPair("X1~X35",fiftyGenes, conditions=tinyCond, pch=20, xlim=c(-4,4), ylim=c(-4,4))