plot_qtl_info: Plot QTLs information from the find_genes_qtls_around_markers...

In GALLO: Genomic Annotation in Livestock for Positional Candidate LOci

Plot QTLs information from the find_genes_qtls_around_markers output

Description

Takes the output from find_genes_qtls_around_markers and create plots for the frequency of each QTL type and trait

Usage

plot_qtl_info(
  qtl_file,
  qtl_plot = c("qtl_type", "qtl_name"),
  n = "all",
  qtl_class = NULL,
  horiz = FALSE,
  ...
)

Arguments

qtl_file	The output from find_genes_qtls_around_markers function
qtl_plot	"qtl_type" or"qtl_name"
n	Number of QTLs to be plotted when the qtl_name option is selected
qtl_class	Class of QTLs to be plotted when the qtl_name option is selected
horiz	The legend of the pie plot for the qtl_type should be plotted vertically or horizontally. The default is FALSE. Therefore, the legend is plotted vertically.
...	Arguments to be passed to/from other methods. For the default method these can include further arguments (such as axes, asp and main) and graphical parameters (see par) which are passed to plot.window(), title() and axis.

Value

A plot with the requested information

Examples

data(QTLmarkers)
data(gffQTLs)

out.qtls<-find_genes_qtls_around_markers(db_file=gffQTLs,
marker_file=QTLmarkers, method = "qtl",
marker = "snp", interval = 500000,
nThreads = 1)

plot_qtl_info(out.qtls, qtl_plot = "qtl_type", cex=2)

GALLO documentation built on June 22, 2024, 9:17 a.m.