R: Initialize circular plot with any genomic data

circos.genomicInitialize {circlize} | R Documentation

## Initialize circular plot with any genomic data

### Description

Initialize circular plot with any genomic data

### Usage

    circos.genomicInitialize(data, sector.names = NULL, major.by = NULL,
        plotType = c("axis", "labels"), tickLabelsStartFromZero = TRUE,
        track.height = convert_height(3, "mm"), ...)

### Arguments

`data` | A data frame containing genomic data.
`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.
`track.height` | If `PlotType` is not `NULL`, height of the annotation track.
`...` | Pass to `circos.initialize`

### Details

The function will initialize circular plot from genomic data. If `plotType` is set with value in `axis` or `labels`, there will create a new track.

The order of sectors related to data structure of `data`. If the first column in `data` is a factor, the order of sectors is `levels(data[[1]])`; If the first column is just a simple vector, the order of sectors is `unique(data[[1]]`.

For more details on initializing genomic plot, please refer to the vignettes.

### References

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

### Examples

    ## Not run:

    df = read.cytoband()$df
    circos.genomicInitialize(df)

    df = data.frame(name = c("TP53", "TP63", "TP73"),
                     start = c(7565097, 189349205, 3569084),
                     end = c(7590856, 189615068, 3652765),
                     stringsAsFactors = FALSE)
    circos.genomicInitialize(df)
    circos.clear()

    circos.genomicInitialize(df, major.by = 10000)
    circos.clear()

    circos.genomicInitialize(df, plotType = "labels")
    circos.clear()

    circos.genomicInitialize(df, sector.names = c("tp53", "tp63", "tp73"))
    circos.clear()

    circos.genomicInitialize(df, sector.names = c("tp53x", "tp63x", "tp73"))
    circos.clear()

    df[[1]] = factor(df[[1]], levels = c("TP73", "TP63", "TP53"))
    circos.genomicInitialize(df)
    circos.clear()

    ## End(Not run)

[Package circlize version 0.4.1 Index]