garfield.plot {garfield} | R Documentation

## Garfield plotting function

### Description

`garfield.plot` is used for visualization of the enrichment analysis results obtained by the `garfield.run` permutation step. Internally, it uses `garfield.plot.fnx` which has been adapted from the 'radial.plot' function from the 'plotrix' package.

### Usage

        garfield.plot(input_file, num_perm = 100000, output_prefix = "plot",
            plot_title = "", filter = 10, tr = Inf)

### Arguments

`input_file` | Input file name as produced by garfield.run permutation step.
`num_perm` | Number of permutations used in the garfield.run permutation step.
`output_prefix` | Figure file prefix. This would create the following files output_prefix.Chromatin_States.pdf, output_prefix.Footprints.pdf, output_prefix.Histone_Modifications.pdf, output_prefix.Peaks.pdf, output_prefix.FAIRE.pdf, output_prefix.Genic.pdf, output_prefix.Hotspots.pdf and output_prefix.TFBS.pdf
`plot_title` | Optional figure title
`filter` | Optional filter for the minimum number of variants at a given threshold. Minimum of 1 should be used, but advisable to set to a larger value (e.g. 10).
`tr` | Threshold for denoting significance of an observed enrichment on a -log10 scale. A value of Inf denotes using default threshold of -log10(0.05/498).

### Details

This function is used for visualization of the enrichment analysis results and produces pdf figures for each class of annotations. Each figure shows the FE values (radial values) at different GWAS thresholds (bottom legend) for each annotation (outer circle and right legend). It further shows the significance at the top 4 GWAS thresholds (if present) as dots on the outer circle, with the most stringent threshold being shown at the inner most side.

### Value

No value is produced, instead output files are generated. See Details and 'output_prefix' for more information.

### Author(s)

Sandro Morganella <email: sm22@sanger.ac.uk>

Maintainer: Valentina Iotchkova <email: vi1@sanger.ac.uk>

### References

Valentina Iotchkova, Graham Ritchie, Matthias Geihs, Sandro Morganella, Josine Min, Klaudia Walter, Nicholas Timpson, UK10K Consortium, Ian Dunham, Ewan Birney and Nicole Soranzo. GARFIELD - GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction. In preparation

### See Also

`garfield.run`, `garfield`, `garfield.plot.fnx`

### Examples

    garfield.run("tmp", data.dir=system.file("extdata",package = "garfield"),
        trait="trait",run.option = "prep", chrs = c(22),
        exclude = c(895, 975, 976, 977, 978, 979, 98))

    garfield.run("tmp", data.dir=system.file("extdata",package = "garfield"),
        trait="", run.option = "perm", nperm = 1000,
        thresh = c(0.001, 1e-04, 1e-05), pt_thresh = c(1e-04, 1e-05),
        maf.bins = 2, tags.bins = 3, tss.bins = 3, prep.file = "tmp.prep",
        optim_mode = TRUE, minit = 100, thresh_perm = 0.05)

    garfield.plot("tmp.perm", num_perm = 1000, output_prefix = "tmp",
        plot_title = "Sample run", filter = 1, tr = -log10(0.05))
    #system("ls -lh tmp.*.pdf")

[Package garfield version 1.18.0 Index]