massiR (version 1.8.0)

massi_cluster_plot: massi_cluster_plot

Description

This function produces three figures in a new graphics device to enable the exploration of the massi_cluster and massi_select results.

Usage

massi_cluster_plot(massi_select_data, massi_cluster_data)

Arguments

massi_select_data

A data.frame containing the subset of y chromosome probe values for each sample. This is returned when running the massi_select function.

massi_cluster_data

This is the list returned from the massi_cluster function.

Value

Returns three plots in a new graphics device.

Details

The first figure is a heatmap depicting probe values for each sample. The second figure is a bar plot showing the mean probe expression and standard deviation for each sample. The bars are colored with respect to the predicted sex. The third figure is a principal component plot which represents the distances bewteen samples, with each cluster highlighted with elipses.

References

Gregory R. Warnes, Ben Bolker, Lodewijk Bonebakker, Robert Gentleman, Wolfgang Huber Andy Liaw, Thomas Lumley, Martin Maechler, Arni Magnusson, Steffen Moeller, Marc Schwartz and Bill Venables (2013). gplots: Various R programming tools for plotting data. R package version 2.12.1. http://CRAN.R-project.org/package=gplots

See Also

massi_cluster, massi_select

Examples

# load the test dataset
data(massi.test.dataset, massi.test.probes)

# select the y chromosome probes using massi_select
massi_select_out <- 
massi_select(massi.test.dataset, massi.test.probes)

# cluster samples to predict sex using massi_cluster
massi_cluster_out <- 
massi_cluster(massi_select_out)

# produce plots using massi_cluster_plot
massi_cluster_plot(massi_select_out, massi_cluster_out)