# Plot.RM.Barchart: 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 barchart.

## Usage

 ```1 2``` ``` Plot.RM.Barchart(group.data, groups, times, plotByGrp = TRUE, col = NULL, conf = .95) ```

## 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. `plotByGrp` When 'TRUE', the plot will be split by group rather than time. `col` A vector of colors to use to denote taxa. `conf` The desired confidence limits. The default is 95%

## Value

A barchart 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 by Group Plot.RM.Barchart(group.data, groups, times) ### Plot the data by Time Plot.RM.Barchart(group.data, groups, times, FALSE) ## End(Not run) ```

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