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Create a QC Manhattan plots from rTASSEL association output

Source: R/plot_manhattan_qc.R
plotManhattanQC.Rd

This function allows for quick generation of a QC plot from rTASSEL association statistical output data. The main goal of this function is to provide "zoomed" in Manhattan plots that typically fall within genomic ranges of interest plus a flanking window up- and downstream of the ranges.

Usage

plotManhattanQC(
  assocRes,
  trait = NULL,
  gr,
  window = 1e+05,
  threshold = NULL,
  classicNames = FALSE,
  interactive = FALSE,
  verbose = TRUE
)

Arguments

assocRes

An object of type AssociationResults

trait

Which phenotypic trait do you want to plot? If set to NULL, this will generate a faceted plot with all mapped traits.

gr

Genomic ranges of interest. Can be passed as a GRanges object or a data.frame object.

window

Window size (base-pairs) flanking surround reference range. Defaults to 100000 (100,000 base-pairs).

threshold

User-defined \(-log_{10}(p)\)-value threshold for significant marker determination. Once specified any marker points higher than this line will be highlighted.

classicNames

Do you want to plot classical gene names instead? NOTE: this will need a classical_id column for the "ranges of interest" data. Defaults to FALSE.

interactive

Do you want to produce an interactive visualization? Defaults to FALSE.

verbose

Should messages be printed to console? Defaults to FALSE.

Value

Returns a ggplot2 object