Plot.RM.Dotplot function

Plot the Pi Vector for Repeated Measures

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

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.

Returns

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)