dandelion.plot: dandelion.plots

In jianhong/trackViewer: A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data

dandelion.plots

Description

Plot variants and somatic mutations

Usage

dandelion.plot(
  SNP.gr,
  features = NULL,
  ranges = NULL,
  type = c("fan", "circle", "pie", "pin"),
  newpage = TRUE,
  ylab = TRUE,
  ylab.gp = gpar(col = "black"),
  xaxis = TRUE,
  xaxis.gp = gpar(col = "black"),
  yaxis = FALSE,
  yaxis.gp = gpar(col = "black"),
  legend = NULL,
  cex = 1,
  maxgaps = 1/50,
  heightMethod = NULL,
  label_on_feature = FALSE,
  ...
)

Arguments

SNP.gr	A object of GRanges or GRangesList. All the width of GRanges must be 1.
features	A object of GRanges or GRangesList.
ranges	A object of GRanges or GRangesList.
type	Character. Could be fan, circle, pie or pin.
newpage	plot in the new page or not.
ylab	plot ylab or not. If it is a character vector, the vector will be used as ylab.
ylab.gp, xaxis.gp, yaxis.gp	An object of class gpar for ylab, xaxis or yaxis.
xaxis, yaxis	plot xaxis/yaxis or not. If it is a numeric vector with length greater than 1, the vector will be used as the points at which tick-marks are to be drawn. And the names of the vector will be used to as labels to be placed at the tick points if it has names.
legend	If it is a list with named color vectors, a legend will be added.
cex	cex will control the size of circle.
maxgaps	maxgaps between the stem of dandelions. It is calculated by the width of plot region divided by maxgaps. If a GRanges object is set, the dandelions stem will be clustered in each genomic range.
heightMethod	A function used to determine the height of stem of dandelion. eg. Mean. Default is length.
label_on_feature	Labels of the feature directly on them. Default FALSE.
...	not used.

Details

In SNP.gr and features, metadata of the GRanges object will be used to control the color, fill, border, height, data source of pie if the type is pie.

Examples

SNP <- c(10, 100, 105, 108, 400, 410, 420, 600, 700, 805, 840, 1400, 1402)
SNP.gr <- GRanges("chr1", IRanges(SNP, width=1, names=paste0("snp", SNP)), 
                  score=sample.int(100, length(SNP))/100)
features <- GRanges("chr1", IRanges(c(1, 501, 1001), 
                                    width=c(120, 500, 405),
                                    names=paste0("block", 1:3)),
                    color="black",
                    fill=c("#FF8833", "#51C6E6", "#DFA32D"),
                    height=c(0.1, 0.05, 0.08))
dandelion.plot(SNP.gr, features, type="fan")

jianhong/trackViewer documentation built on Dec. 10, 2024, 10:33 a.m.