Create a heatmap to visualize and compare the genetic genetic backgrounds of genotypes/lines with or without annotation for introgressed loci.

Usage

cross_qc_heatmap(
  x,
  map_file,
  snp_ids = "snpid",
  chr = "chr",
  chr_pos = "pos",
  parents,
  trait_pos = NULL,
  group_sz = nrow(x) - 2,
  pdf = FALSE,
  filename = "background_heatmap",
  legend_title = "Heatmap_key",
  col_mapping,
  col_labels,
  panel_fill = "grey80",
  panel_col = "white",
  alpha = 0.9,
  text_size = 12,
  text_scale_fct = 0.5,
  width = 9,
  height = 6.5,
  label_offset = -1,
  ...
)

Arguments

x: A numeric matrix with marker IDs as columns and sample IDs as row names.
map_file: A data frame of map file consisting of SNP IDs and their chromosome numbers and positions as columns.
snp_ids: A character value indicating the column name for marker IDs in x.
chr: A character value indicating the column name for chromosome IDs in x.
chr_pos: A character value indicating the column name for chromosome positions in x.
parents: A character vector of length = 2 for the IDs of parents.
trait_pos: A list object where the components correspond to the chromosome number, start and end positions of trait loci to annotate on the heapmap.
group_sz: A positive integer value indicating the batch size for progenies to include in heatmap.
pdf: A logical value indicating whether to save plot as a pdf graphic device when TRUE or output plot in R when FALSE.
filename: A character value for path or file name for saving pdf.
legend_title: A character value for specifying plot legend title.
col_mapping: A character vector of length = 6 for heatmap color mapping.
col_labels: A character vector of length = 6 for labels corresponding to the color mapping.
panel_fill: A character value for setting the panel background fill color.
panel_col: A character value for setting the panel background border color.
alpha: A numeric value between 0 and 1 for modifying the opacity of colors.
text_size: A numeric value for setting text size.
text_scale_fct: A numeric value for scaling text size. The default value is `50%` of the defined text size.
width: A numeric value for the width of pdf device.
height: A numeric value for the height of pdf device.
label_offset: A numeric value indicating the position of the trait loci text labels on the heatmap. It is positioned on the donor parent by default.
...: Other valid arguments that can be passed to ggplot2.

Value

A ggplot graphical object.

Examples

# \donttest{
# example code
library(panGenomeBreedr)
# Create a numeric matrix of genotype scores for 10 markers and 5 samples
num_dat <- matrix(c(rep(1, 10), rep(0, 10),
                    1, 1, 0.5, 1, 1, 1, 1, 1, 0, 1,
                    1, 1, 0, 1, 1, 1, 1, 1, 1, 1,
                    1, 1, 0, 1, 1, 1, 1, 1, 1, 0.5 ),
                  byrow = TRUE, ncol = 10)

rownames(num_dat) <- c('rp', 'dp', paste0('bc1_', 1:3))
colnames(num_dat) <- paste0('S1', '_', c(floor(seq(1000, 10000, len = 8)),
                                         15000, 20000))

# Get map file by parsing SNP IDs
map_file <- parse_marker_ns(colnames(num_dat))

# Annotate a heatmap to show trait loci positions
cross_qc_heatmap(x = num_dat,
                map_file = map_file,
                snp_ids = 'snpid',
                chr = 'chr',
                chr_pos = 'pos',
                parents = c('rp', 'dp'),
                trait_pos = list(loc1 = c(chr = 1, start = 2900, end = 4200),
                loc2 = c(chr = 1, start = 14200, end = 15800)),
                text_scale_fct = 0.5,
                group_sz = 3L,
                pdf = FALSE,
                legend_title = 'BC1',
                alpha = 0.8,
                text_size = 15)
#> $Batch1

#> 

# }