View source: R/PlotFunctions.R
plotDosage | R Documentation |
This function counts a reference allele dosage per marker per sample and draw line plots of them in facets for each chromosome for each sample.
plotDosage(
x,
coord = NULL,
chr = NULL,
ind = 1,
node = "raw",
showratio = TRUE,
dot_fill = c("green", "darkblue"),
size = 0.8,
alpha = 0.8,
line_color = "magenta"
)
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 |
An index to specify samples to be drawn. |
node |
Either one of "raw", "filt", and "cor" to output raw genotype data, filtered genotype data, or corrected genotype data, respectively. |
showratio |
If |
dot_fill |
A string to indicate the dot color in a plot. |
size |
A positive number to indicate the dot size in a plot. |
alpha |
A positive number in 0-1 to indicate the dot opacity in a plot. |
line_color |
A string to indicate the line color in the plot. |
A ggplot object.
# Load data in the GDS file and instantiate a [GbsrGenotypeData] object.
gds_fn <- system.file("extdata", "sample.gds", package = "GBScleanR")
gds <- loadGDS(gds_fn)
plotDosage(gds, ind = 1)
# Close the connection to the GDS file
closeGDS(gds)
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