Plot.RM.Dotplot: Plot the Pi Vector for Repeated Measures

In HMP: Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP

Description

Plots the taxa proportions for every group/time as a dot plot.

Usage

	Plot.RM.Dotplot(group.data, groups, times, errorBars = TRUE, 
		col = NULL, conf = .95, alpha = 1)

Arguments

group.data	A list of matrices of taxonomic counts(columns) for each sample(rows).
groups	A vector indicating group membership.
times	A vector indicating time.
errorBars	When 'TRUE', error bars will also be displayed.
col	A vector of colors to use to denote taxa.
conf	The desired confidence limits. The default is 95%
alpha	The desired alpha level for the colors.

Value

A plot of the pi vectors for every group/time.

Examples

	## Not run: 
		data(saliva)
		data(throat)
		
		### Reduce the size of the data
		saliva <- Data.filter(saliva, numTaxa=9)
		throat <- Data.filter(throat, numTaxa=9)
		
		### Get the gamma value for the data
		saliva.gamma <- DM.MoM(saliva)$gamma
		throat.gamma <- DM.MoM(throat)$gamma
		mid.gamma <- (saliva.gamma + throat.gamma)/2
		
		### Generate a the number of reads per sample
		### The first number is the number of reads and the second is the number of subjects
		nrs <- rep(10000, 20)
		
		### Create data sets to be our time series in a list
		group.data <- list(
				Dirichlet.multinomial(nrs, saliva.gamma),
				Dirichlet.multinomial(nrs, saliva.gamma),
				Dirichlet.multinomial(nrs, saliva.gamma),
				Dirichlet.multinomial(nrs, saliva.gamma),
				Dirichlet.multinomial(nrs, mid.gamma),
				Dirichlet.multinomial(nrs, throat.gamma)
		)
		names(group.data) <- c(
				"Group 1, Time 1", "Group 2, Time 1",
				"Group 1, Time 2", "Group 2, Time 2",
				"Group 1, Time 3", "Group 2, Time 3"
		)
		
		### Set the group and time information for each list element
		groups <- c(1, 2, 1, 2, 1, 2)
		times <- c(1, 2, 3, 1, 2, 3)
		
		### Plot the data with error bars
		Plot.RM.Dotplot(group.data, groups, times)
		
		### Plot the data without error bars
		Plot.RM.Dotplot(group.data, groups, times, FALSE)
	
## End(Not run)

HMP documentation built on Aug. 31, 2019, 5:05 p.m.