scatterplot: Plot beta values of individual CpG sites against the independent variable.

Description

Plot beta values of individual CpG sites against the independent variable. Can create scatterplots and boxplots. If scatterplots the intercept will be adjusted for any covariates that were included in the model. Only available if return.data was set to T.

Usage

scatterplot(x, cpg.rank = NULL, cpg.name = NULL, save.plot = NULL, file.type="pdf", 
eps.size = c(5, 5), popup.pdf = FALSE, beta.values = NULL,
user.indep=NULL,main.title=NULL, ...)

Arguments

x: Object of class "cpg" or "cpg.perm".
cpg.rank: A vector listing the rank of sites to be plotted. The rank is based on the ordered p-values.
cpg.name: A character vector containing the names of CpG sites to be plotted against the phenotype of interest. This option is ignored if cpg.rank is specified.
save.plot: Prefix of the filename for the plot(s) to be saved to. If specified, plot filenames will be created by appending this prefix to either cpg.rank or cpg.name. If not specified, plot will not be saved.
file.type: Type of file to be saved. Can either be "pdf" or "eps". Selecting file.type="eps" will result in publication quality editable postscript files that can be opened by Adobe Illustrator or Photoshop.
eps.size: Vector indicating the size of .eps file (if creating one). Corresponds to horizontal and height.
popup.pdf: TRUE or FALSE. If creating a pdf file, this indicates if the plot should appear in a popup window as well. If running in a cluster-like environment, best to leave FALSE.
beta.values: If the object has been renamed (i.e. x$info$betainfo is no longer in ls(.GlobalEnv)) then specify the new object here.
user.indep: Default NULL. If return.data=F in run, scatterplot will not work. Pass in samplepheno here. Must be in same order as samplecpg.
main.title: Main title to be put on the graph. If NULL one based on the analysis will be used.
...: Arguments to be passed to methods, such as graphical parameters.

Author

Barfield, R.; Kilaru,V.; Conneely, K.
Maintainer: R. Barfield: <barfieldrichard8@gmail.com>

Details

An unlimited number of CpG sites can be selected for plotting by specifying either cpg.rank or cpg.name, as shown in the Examples below. Note that only one of these options is needed; if both are entered, cpg.rank will be used.

Examples

Run this code

#Load the data:
data(samplecpg,samplepheno,package="CpGassoc")

test<-cpg.assoc(samplecpg,samplepheno$weight,large.data=FALSE,return.data=TRUE)
##Using rank, will plot the top three sites in order of significance:
scatterplot(test,c(1:3),user.indep=sampleoheno$weight)
##Using name, specify three sites:
scatterplot(test,cpg.name=c("CpG1182","CpG1000","CpG42"))

##Plotting something that is categorical in nature:
test2<-cpg.assoc(samplecpg[1:200,],factor(samplepheno$Disease),large.data=FALSE,return.data=TRUE)
scatterplot(test2,c(2),beta.values=samplecpg[1:200,],
user.indep=sampleoheno$weight)