plotReadRatio: Draw line plots of proportion of reference allele read counts...

In tomoyukif/GBScleanR: Error correction tool for noisy genotyping by sequencing (GBS) data

Draw line plots of proportion of reference allele read counts per marker per sample.

Description

This function calculate a proportion of reference allele read counts per marker per sample and draw line plots of them in facets for each chromosome for each sample.

Usage

plotReadRatio(
  x,
  coord = NULL,
  chr = NULL,
  ind = 1,
  node = "raw",
  dot_fill = c("green", "darkblue"),
  size = 0.8,
  alpha = 0.8
)

Arguments

x	A GbsrGenotypeData object.
coord	A vector with two integer specifying the number of rows and columns to draw faceted line plots for chromosomes.
chr	A vector of indexes to specify chromosomes to be drawn.
ind	A string of sample id or an index to specify the sample to be drawn.
node	Either one of "raw" or "filt" to output raw read data, or filtered read data, respectively.
dot_fill	A vector of two strings to indicate the dot colors in the plot. The first and second elements of the vector are set as the colors for the lowest and highest values in the gradient coloring of the dots indicating total read counts par marker.
size	A positive number to indicate the dot size in the plot.
alpha	A positive number in 0-1 to indicate the dot opacity in the plot.

Value

A ggplot object.

Examples

# Load data in the GDS file and instantiate a [GbsrGenotypeData] object.
gds_fn <- system.file("extdata", "sample.gds", package = "GBScleanR")
gds <- loadGDS(gds_fn)

plotReadRatio(gds, ind = 1)

# Close the connection to the GDS file
closeGDS(gds)

tomoyukif/GBScleanR documentation built on Oct. 31, 2024, 2:43 a.m.