circular layout of more than one panlemaps

circomap plots multiple cohorts having grouped data in the form of a panelmap laid out in a circular fashion. Each pie reflects the relative size of each cohort, and each track is a panelet summarizing a feature.

circomap(datasets,gtoplot,gcol,gheight,ftoplot,ftype,fcol,fheight,
NA.flag="FALSE",NA.col="grey")

Arguments

datasets	list. Arrange the datasets to plot in a list. Each dataset has samples as columns and features as rows. The row features should be uniform across datasets. See example below. The dataset is sorted according to the group variable and is included in the dataset.
gtoplot	character. Name of the group variable to plot.
gcol	vector. Color to be assigned to each group in group labels.
gheight	numeric. Height of the group label panelet track. Default is 0.10
ftoplot	vector. Names of the features to plot. See example
ftype	vector. Type of data type to be plotted in ftoplot. 1 = discrete/binary. 2 = continuous .See example below and makepanel.
fcol	list. A list of color values to be coded. Names of the list are same as ftoplot see example below and makepanel.
fheight	numeric. Height of each of the panelet track.
NA.flag	logical. default is FALSE. If there are NAs in your categories set it as TRUE
NA.col	character. Default is "grey". Set the color for NAs

Details

The radius of circomap is 1. Heights of gheight and fheight should be chosen accordingly.

Value

returns a circomap

References

Gu, Z. circlize implements and enhances circular visualization in R. Bioinformatics 2014.

See also

makepanel

Examples

#dataset 1
dat1 = mtcars[order(mtcars$cyl),]
#dataset 2
dat2 = mtcars[order(mtcars$cyl),]
#dataset 3
dat3 = mtcars[order(mtcars$cyl),]

#put all the datasets in a list
datasets<-list()
datasets[[1]]=dat1; datasets[[2]]=dat2; datasets[[3]]=dat3
names(datasets) = c("dat1", "dat2", "dat3")
#names of datasets will be used to labek the datasets

#group variable to plot same as panelet_group
gtoplot<-c("cyl")
gcol = c("red","blue","green")
gheight = 0.10 #track height of the group variable

#features to plot - same as in panelmap example
ftoplot<-c("mpg", "vs", "am", "gear")
ftype= c(2,1,1,1)
fcol=list(am=c("white","black"), vs=c("white","black"),
gear=c("yellow","orange","brown"), mpg=c("white", "darkred"))

fheight<-list(); fheight[1:length(ftoplot)] = 0.08
#Voila!!
circomap(datasets, gtoplot, gcol, gheight, ftoplot, ftype, fcol, fheight)
#> Note: 1 point is out of plotting region in sector 'dat1', track '1'.
#> Note: 1 point is out of plotting region in sector 'dat2', track '1'.
#> Note: 1 point is out of plotting region in sector 'dat3', track '1'.