# 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

 1 2 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

 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 ## 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.