Create decision support bar plots of match vs. mismatch rates of KASP markers that had predictions for positive controls.

Usage

pred_summary_plot(
  x,
  pdf = FALSE,
  pred_cols = c(false = "red", true = "blue", unverified = "orange2"),
  filename = "pred_summary_barplot",
  alpha = 1,
  text_size = 12,
  width = 6,
  height = 6,
  angle = 45,
  ...
)

Arguments

x: A data frame object of prediction summaries of KASP markers returned by the `pred_summary()` function.
pdf: A logical value indicating whether to save plot as a pdf graphic device when TRUE or output plot in R when FALSE.
pred_cols: A named character vector of length = 3 of colors to be used for the prediction status legend for positive controls.
filename: A character value for path or file name for saving pdf.
alpha: A numeric value between 0 and 1 for modifying the opacity of colors.
text_size: A numeric value for setting text size.
width: A numeric value for the width of pdf device.
height: A numeric value for the height of pdf device.
angle: A numeric value for setting the angle placement for text on the axis.
...: Other valid arguments that can be passed to ggplot2.

Value

A graphic object or ggplot.

Examples

# \donttest{
# example code
library(panGenomeBreedr)
dat1 <- panGenomeBreedr::beta_carotene
my_sum <- kasp_color(x = dat1,
                        subset = 'plates',
                        sep = ':',
                        geno_call = 'Call',
                        uncallable = 'Uncallable',
                        unused = '?',
                        blank = 'NTC') |>

pred_summary(snp_id = 'SNPID',
               Group_id = 'Group',
               Group_unknown = '?',
               geno_call = 'Call',
               rate_out = TRUE)

pred_summary_plot(x = my_sum$summ,
                  pdf = FALSE,
                  pred_cols = c('false' = 'red', 'true' = 'blue',
                                'unverified' = 'orange2'),
                  alpha = 1,
                  text_size = 12,
                  width = 6,
                  height = 6,
                  angle = 45)
#> $snpSB00800

#> 
#> $snpSB00803

#> 
#> $snpSB00804

#> 
#> $snpSB00805

#> 
# }