Object ccPlot calls one of the following functions based on the value of initMode: circlize::circos.initialize, circlize::circos.genomicInitialize, circlize::circos.initializeWithIdeogram, circlize::circos.heatmap.initialize.
Usage
ccPlot(initMode = 'initialize',clear = TRUE,sectors = NULL,x = NULL,xlim = NULL,sector.width = NULL,factors = sectors,ring = FALSE)
ccPlot(initMode = 'genomicInitialize',clear = TRUE,data=NULL,sector.names = NULL,major.by = NULL,plotType = c("axis", "labels"),tickLabelsStartFromZero = TRUE,axis.labels.cex = 0.4*par("cex"),labels.cex = 0.8*par("cex"),track.height = NULL,...)
ccPlot(initMode = 'initializeWithIdeogram',clear = TRUE,cytoband = system.file(package = "circlize", "extdata", "cytoBand.txt"),species = NULL,sort.chr = TRUE,chromosome.index = usable_chromosomes(species),major.by = NULL,plotType = c("ideogram", "axis", "labels"),track.height = NULL,ideogram.height = convert_height(2, "mm"),...)
ccPlot(initMode = 'heatmap.initialize',clear = TRUE,mat=NULL, split = NULL, cluster = TRUE,clustering.method = "complete", distance.method = "euclidean",dend.callback = function(dend, m, si) reorder(dend, rowMeans(m)),cell_width = rep(1, nrow(mat)))Arguments
- initMode
It can only be the following values: "initialize", "genomicInitialize", "initializeWithIdeogram", "heatmap.initialize".
- clear
Whether to call circlize::circos.clear after drawing.
- ...
Parameters passed to the function in the package circlize. The function is one of the following four:circlize::circos.initialize, circlize::circos.genomicInitialize, circlize::circos.initializeWithIdeogram, circlize::circos.heatmap.initialize.
Examples
n = 1000
df = data.frame(sectors = sample(letters[1:8], n, replace = TRUE),
x = rnorm(n), y = runif(n))
library(circlizePlus)
cc=ccPlot(initMode = 'initialize', sectors = df$sectors, x = df$x)