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Last data update: 2014.03.03

R: Pairs Plot for DEDS Objects

pairs-methods

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 regression 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 would 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.

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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(DEDS)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DEDS/pairs.DEDS.Rd_%03d_medium.png", width=480, height=480)
> ### Name: pairs-methods
> ### Title: Pairs Plot for DEDS Objects
> ### Aliases: pairs.DEDS pairs pairs-methods
> ### Keywords: hplot
> 
> ### ** 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)
We'll do random permutations, B =  200 

Two-sample Statistics:
t 	FC 	SAM 	
E of the orginial data is: 5.698  1.736  2.846  
b=2	b=4	b=6	b=8	b=10	b=12	b=14	b=16	b=18	b=20	
b=22	b=24	b=26	b=28	b=30	b=32	b=34	b=36	b=38	b=40	
b=42	b=44	b=46	b=48	b=50	b=52	b=54	b=56	b=58	b=60	
b=62	b=64	b=66	b=68	b=70	b=72	b=74	b=76	b=78	b=80	
b=82	b=84	b=86	b=88	b=90	b=92	b=94	b=96	b=98	b=100	
b=102	b=104	b=106	b=108	b=110	b=112	b=114	b=116	b=118	b=120	
b=122	b=124	b=126	b=128	b=130	b=132	b=134	b=136	b=138	b=140	
b=142	b=144	b=146	b=148	b=150	b=152	b=154	b=156	b=158	b=160	
b=162	b=164	b=166	b=168	b=170	b=172	b=174	b=176	b=178	b=180	
b=182	b=184	b=186	b=188	b=190	b=192	b=194	b=196	b=198	b=200	

After permutation , E is set at: 6.756  1.736  2.846  

Summarizing DEDS results for 200 permutations and 100 genes, please wait... 
> 
> # 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)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>