onemap (version 2.1.1)

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

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 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

# NOT RUN {
# }
# NOT RUN {
data(mapmaker_example_bc) # Loads a fake backcross dataset installed with onemap
plot(mapmaker_example_bc) # This will show you the graph

# You can store the graphic in an object, then save it with a number of properties
# For details, see the help of ggplot2's function ggsave()
g <- plot(mapmaker_example_bc)
ggplot2::ggsave("MyRawData_bc.jpg", g, width=7, height=4, dpi=600)

data(onemap_example_f2) # Loads a fake backcross dataset installed with onemap
plot(onemap_example_f2) # This will show you the graph

# You can store the graphic in an object, then save it with a number of properties
# For details, see the help of ggplot2's function ggsave()
g <- plot(onemap_example_f2)
ggplot2::ggsave("MyRawData_f2.jpg", g, width=7, height=4, dpi=600)

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)
ggplot2::ggsave("MyRawData_out.jpg", g, width=9, height=4, dpi=600)
# }