Make KASP marker genotyping QC plot overlaid with predicitons.

Usage

kasp_qc_ggplot2(
  x,
  FAM = "X",
  HEX = "Y",
  geno_call = "Call",
  color = "Color",
  PCH = "pch",
  snp_id = "SNPID",
  blank = "NTC",
  uncallable = "Uncallable",
  unused = "?",
  others = c("Missing", "Bad", "Dupe", "Over", "Short"),
  Group_id = NULL,
  Group_unknown = "?",
  pred_cols = c(Blank = "black", False = "red", True = "blue", Unverified = "orange2"),
  scale = FALSE,
  pdf = TRUE,
  width = 6,
  height = 6,
  filename = "kasp_qc",
  expand_axis = 0.5,
  legend.pos.x = 0.6,
  legend.pos.y = 0.75,
  legend.box = "horizontal",
  legend.pos = "inside",
  alpha = 0.9,
  text_size = 12,
  ...
)

Arguments

x: A list object of KASP genotype calls processed by the `kasp_color()` function.
FAM: A character indicating the column name for FAM fluorescence coordinates in x.
HEX: A character indicating the column name for HEX fluorescence coordinates in x.
geno_call: A character value indicating the column name for KASP genotype calls in x.
color: A character value indicating the column name for assigned colors in x.
PCH: A character value indicating the column name for assigned PCH symbols in x.
snp_id: A character value indicating the column name for SNP IDs in x.
blank: A character value indicating `No Template Controls (NTC)` genotype calls.
uncallable: A character indicating `Uncallable` genotype calls, if present.
unused: A character indicating `?` genotype calls, if present.
others: A character vector indicating other non-genotype calls in KASP genotype calls, if present. These may include `'Missing', 'Bad', 'Dupe'`, `'Over', 'Short'`.
Group_id: A character value for the column ID indicating the predictions of the positive controls in x.
Group_unknown: A character value representing unknown genotype status for samples, if present. No genotype prediction could be made for such samples.
pred_cols: A named character vector of length = 4 of colors to be used for the prediction legend for positive controls, if present.
scale: A logical value indicating whether to scale FAM and HEX axis to values between 0 and 1.
pdf: A logical value indicating whether to save plot as a pdf graphic device when TRUE or output plot in R when FALSE.
width: A numeric value for the width of pdf device.
height: A numeric value for the height of pdf device.
filename: A character value for path or file name for saving pdf.
expand_axis: A numeric value to expand the axes for legend positioning.
legend.pos.x: A numeric value representing the x coordinate for legend placement.
legend.pos.y: A numeric value representing the y coordinate for legend placement.
legend.box: A character value of either `horizontal` or `vertical` legend placement.
legend.pos: A character value for the position of legend; the default value is `inside`.
alpha: A numeric value between 0 and 1 for modifying the opacity of colors.
text_size: A numeric value for setting text size.
...: Other valid arguments that can be passed to ggplot2.

Value

A graphic object or plot.

Examples

# example code
library(panGenomeBreedr)
# \donttest{
# Assign KASP colors to plates
dat1 <- kasp_color(x = panGenomeBreedr::kasp_dat,
                   subset = 'MasterPlate',
                   sep = ':',
                   geno_call = 'Call',
                   uncallable = 'Uncallable',
                   unused = '?',
                   blank = 'NTC')
#> Marker in Plate SE-24-0392_P01_d2 failed! Check genotype calls.
#> Marker in Plate SE-24-0392_P01_d1 failed! Check genotype calls.
#> Marker in Plate SE-24-0395_P01_d2 failed! Check genotype calls.
#> Marker in Plate SE-24-0395_P01_d1 failed! Check genotype calls.
#> Marker in Plate SE-24-0397_P01_d2 failed! Check genotype calls.
#> Marker in Plate SE-24-0397_P01_d1 failed! Check genotype calls.

# KASP QC plot for Plate 12
kasp_qc_ggplot2(x = dat1[12],
                    pdf = FALSE,
                    Group_id = 'Group',
                    Group_unknown = NULL,
                    scale = TRUE,
                    expand_axis = 0.6,
                    alpha = 0.5,
                    legend.pos.x = 0.6,
                    legend.pos.y = 0.8)
#> $`SE-24-0396_P01_d1`

#> 
# }