plot.onemap: Draw a graphic of raw data for any OneMap population

In bschiffthaler/BatchMap: Software for the Creation of High Density Linkage Maps in Outcrossing Species

Description

Shows a heatmap (in ggplot2, a graphic of geom "tile") for raw data. Lines correspond to markers and columns to individuals. The function can plot a graph for all marker types, depending of the cross type (dominant/codominant markers, in all combinations). The function receives a onemap object of class onemap, reads information from genotypes from this object, converts it to a long dataframe format using function melt() from package reshape2() or internal function create.dataframe.for.plot.outcross(), converts numbers from the object to genetic notation (according to the cross type), then plots the graphic. If there is more than 20 markers, removes y labels For outcross populations, it can show all markers together, or it can split them according the segregation pattern.

Usage

## S3 method for class 'onemap'
plot(x, all = TRUE, ...)

Arguments

x	an object of class onemap, with data and additional information
all	a TRUE/FALSE option to indicate if results will be plotted together (if TRUE) or splitted based on their segregation pattern. Only used for outcross populations.
...	currently ignored

Value

a ggplot graphic

Examples

data(example.out) # Loads a fake full-sib dataset installed with onemap
plot(example.out) # This will show you the graph for all markers
plot(example.out, all=FALSE) # This will show you the graph splitted for marker types

# You can store the graphic in an object, then save it.
# For details, see the help of ggplot2's function ggsave()
g <- plot(example.out, all=FALSE)

bschiffthaler/BatchMap documentation built on Dec. 16, 2019, 2:22 a.m.