plotData {cfda} R Documentation

Plot categorical functional data

Description

Plot categorical functional data

Usage

```plotData(
data,
group = NULL,
col = NULL,
sort = FALSE,
nCol = NULL
)
```

Arguments

 `data` data.frame containing `id`, id of the trajectory, `time`, time at which a change occurs and `state`, associated state. `group` vector, of the same length as the number individuals of `data`, containing group index. Groups are displayed on separate plots. If `group = NA`, the corresponding individuals in `data` is ignored. `col` a vector containing color for each state (can be named) `addId` If TRUE, add id labels `addBorder` If TRUE, add black border to each individual `sort` If TRUE, id are sorted according to the duration in their first state `nCol` number of columns when `group` is given

Value

a `ggplot` object that can be modified using `ggplot2` package. On the plot, each row represents an individual over [0:Tmax]. The color at a given time gives the state of the individual.

Author(s)

Cristian Preda, Quentin Grimonprez

Examples

```# Simulate the Jukes-Cantor model of nucleotide replacement
K <- 4
PJK <- matrix(1/3, nrow = K, ncol = K) - diag(rep(1/3, K))
lambda_PJK <- c(1, 1, 1, 1)
d_JK <- generate_Markov(n = 10, K = K, P = PJK, lambda = lambda_PJK, Tmax = 10)

# add a line with time Tmax at the end of each individual
d_JKT <- cut_data(d_JK, Tmax = 10)

plotData(d_JKT)

# modify the plot using ggplot2
library(ggplot2)
plotData(d_JKT, col = c("red", "blue", "green", "brown")) +
labs(title = "Trajectories of a Markov process")

# use the group variable: create a group with the 3 first variables and one with the others
group <- rep(1:2, c(3, 7))
plotData(d_JKT, group = group)

# use the group variable: remove the id number 5 and 6
group[c(5, 6)] = NA
plotData(d_JKT, group = group)

```

[Package cfda version 0.9.9 Index]