pairs-methods {DEDS}R Documentation

Pairs Plot for DEDS Objects

Description

The function pairs-DEDS produces pairs plots of statistics or p values for DEDS-class objects.

Usage

## S3 method for class 'DEDS':
pairs(x, subset=c(1:nrow(x$stats)), labels =
colnames(x$stats[,-1]), logit = FALSE,
diagonal = c("qqnorm", "boxplot", "density", "histogram", "none"),
lower = c("cor", "none"), groups.by.deds = TRUE, thresh = 0.05, reg.line
= NULL, smooth = FALSE, line.by.group = FALSE, diag.by.group = TRUE, lower.by.group =
FALSE, col = palette(), pch = 1:n.groups, lwd = 1, legend.plot =
length(levels(groups)) > 1, ...)

Arguments

x An object of DEDS.
subset A numeric vector indicating the subset of points to be plotted.
labels A character vector specifying the names of the variables.
logit A logical variable, if TRUE the variables are logged, useful when plotting p values.
diagonal A character string specifying the type of plot to be applied in the diagonal panels.
diagonal="qqnorm": qqnorm on the diagonal
diagonal="boxplot": boxplot on the diagonal
diagonal="density": density on the diagonal
diagonal="histogram": hist on the diagonal
diagonal="none": no special plot will be applied on the diagonal
lower A character string specifying the function to be applied in the lower panels.
lower="cor": absolute correlation will be put on the lower panel
none="cor"; no special function will be applied
groups.by.deds A logcial variable, if TRUE, points will be separated into groups according to their magnitude of q- or p-values by DEDS.
thresh A numeric variable, if thresh<1, it specifies the threshold of significance in differential expression (DE) for q- or p-values of the DEDS object; default is set at 0.05. If thresh>1, it specifies the number of top DE genes to be highlighted.
reg.line A function name specifying the type of regressio line to be plotted in the scatter plots. If reg.line=lm, linear regression line will be plotted; If reg.line=NULL, no regression line will be plotted in the scatter plot.
smooth A logical variable specifying if smooth regression lines will be plotted in the scatter plots. If smooth=TRUE, a lowess line will be applied.
line.by.group A logical variable specifying if the regression lines should be applied within groups.
diag.by.group A logical variable specifying if the plot in the diagonal panels whould be applied groupwise.
lower.by.group A logical variable, if lower.by.group=TRUE and lower="cor", correlation coefficients will be calculated and printed separated according to groups in the lower panels.
col A specification for the colors to be used for plotting different groups, see par.
pch A specification for the type of points to be used for plotting different groups, see par.
lwd A specification for the width of lines to be used if lines are plotted; see par.
legend.plot A logical variable specifying if the legend will be plotted.
... Extra parameters for plotting.

Details

The function pairs.DEDS implements a S3 method of pairs for DEDS. The DEDS class is a simple list-based class to store DEDS results and it is usually created by functions deds.pval, deds.stat, deds.stat.linkC. The list contains a "stat" component, which stores statistics or p values from various statistical tests. The function pairs.DEDS extracts the "stat" component and produces a matrix of scatterplot.

pairs.DEDS as a default highlights points (corresponding to genes) with adjusted p- or q-values less than a user defined threshold. The user can select among a series of options a plot for the diagonal panel; as a default, it produces a qqnorm for each column in the "stat" matrix. Both the diagonal and lower panels can be stratified by specifying the diag.by.group or lower.by.group arguments.

Author(s)

Yuanyuan Xiao, yxiao@itsa.ucsf.edu,
Jean Yee Hwa Yang, jean@biostat.ucsf.edu.

See Also

deds.stat, deds.pval, deds.stat.linkC, hist.DEDS, qqnorm.DEDS

Examples

X <- matrix(rnorm(1000,0,0.5), nc=10)
L <- rep(0:1,c(5,5))

# genes 1-10 are differentially expressed
X[1:10,6:10]<-X[1:10,6:10]+1
# DEDS
d <- deds.stat.linkC(X, L, B=200)

# pairs plot
pairs(d)
# plot regression line
pairs(d, reg.line=lm, lwd=2)
# histogram in the diagonal panel
pairs(d, diagonal="hist")
# boxplot on the diagonal panel and stratified
pairs(d, diagonal="boxplot", diag.by.group=TRUE)

[Package DEDS version 1.0.3 Index]