Plot.RM.Dotplot {HMP} | R Documentation |
Plot the Pi Vector for Repeated Measures
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)
[Package HMP version 2.0.1 Index]