pairs-methods {DEDS} | R Documentation |
The function pairs-DEDS
produces pairs plots of statistics or p
values for DEDS-class
objects.
## 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, ...)
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.
| ||||||||||
lower |
A character string specifying the function to be
applied in the lower panels.
| ||||||||||
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. |
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.
Yuanyuan Xiao, yxiao@itsa.ucsf.edu,
Jean Yee Hwa Yang, jean@biostat.ucsf.edu.
deds.stat
, deds.pval
,
deds.stat.linkC
, hist.DEDS
,
qqnorm.DEDS
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)