dandelion.plot {trackViewer} | R Documentation

## 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")

[Package trackViewer version 1.28.1 Index]