circlizePlus (version 0.9.0)

ccPlot: Object generator for S4 class ccPlot

Description

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.
The correct way to call it is as follows:
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)))

Usage

ccPlot(initMode = "initialize", clear = TRUE, ...)

Value

Object ccPlot

Arguments

initMode

It can only be the following values: "initialize", "genomicInitialize", "initializeWithIdeogram", "heatmap.initialize".

clear

Whether to call circlize::circos.clear before drawing.

...

Arguments passed on to circlize::circos.initialize, circlize::circos.genomicInitialize, circlize::circos.initializeWithIdeogram, circlize::circos.heatmap.initialize

sectors

A factor variable or a character vector which represent data categories

factors

The same as sectors. It will be removed in future versions.

x

Data on x-axes, a vector

xlim

Ranges for values on x-axes, see "details" section for explanation of the format

sector.width

Width for each sector. The length of the vector should be either 1 which means all sectors have same width or as same as the number of sectors. Values for the vector are relative, and they will be scaled by dividing their summation. By default, it is NULL which means the width of sectors correspond to the data range in sectors.

ring

Whether the sector represented as a ring. If yes, there should only be one sector in the circle.

data

A data frame in bed format.

sector.names

Labels for each sectors which will be drawn along each sector. It will not modify values of sector index.

major.by

Increment of major ticks. It is calculated automatically if the value is not set (about every 10 degrees there is a major tick).

plotType

If it is not NULL, there will create a new track containing axis and names for sectors. This argument controls which part should be drawn, axis for genomic axis and labels for chromosome names

tickLabelsStartFromZero

Whether axis tick labels start from 0? This will only affect the axis labels while not affect x-values in cells.

axis.labels.cex

The font size for the axis tick labels.

labels.cex

The font size for the labels.

track.height

If PlotType is not NULL, height of the annotation track.

cytoband

A path of the cytoband file or a data frame that already contains cytoband data. By default it is cytoband for hg19. Pass to read.cytoband.

species

Abbreviations of species. e.g. hg19 for human, mm10 for mouse. If this value is specified, the function will download cytoBand.txt.gz from UCSC website automatically. If there is no cytoband for user's species, it will keep on trying to download chromInfo file. Pass to read.cytoband or read.chromInfo.

chromosome.index

subset of chromosomes, also used to reorder chromosomes.

sort.chr

Whether chromosome names should be sorted (first sort by numbers then by letters). If chromosome.index is set, this argumetn is enforced to FALSE

ideogram.height

Height of the ideogram track

mat

A matrix or a vector. The vector is transformed as a one-column matrix.

split

A categorical variable. It splits the matrix into a list of matrices.

cluster

whether to apply clustering on rows. The value can also be a dendrogram/hclust object or other objects that can be converted to with as.dendrogram.

clustering.method

Clustering method, pass to hclust.

distance.method

Distance method, pass to dist.

dend.callback

A callback function that is applied to the dendrogram in every sector.

cell_width

Relative widths of heatmap cells.

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)