massi_cluster_plot {massiR} | R Documentation

## 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.

### 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.

### Value

Returns three plots in a new graphics device.

### Author(s)

Sam Buckberry

### 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)

[Package massiR version 1.20.0 Index]