Plot the optimal encoding
# S3 method for fmca
plot(
x,
harm = 1,
states = NULL,
addCI = FALSE,
coeff = 1.96,
col = NULL,
nx = 128,
...
)Arguments
- x
output of
compute_optimal_encodingfunction- harm
harmonic to use for the encoding
- states
states to plot (default = NULL, it plots all states)
- addCI
if TRUE, plot confidence interval (only when
computeCI = TRUEin compute_optimal_encoding)- coeff
the confidence interval is computed with +- coeff * the standard deviation
- col
a vector containing color for each state
- nx
number of time points used to plot
- ...
not used
Value
a ggplot object that can be modified using ggplot2 package.
Details
The encoding for the harmonic h is \(a_{x}^{(h)} \approx \sum_{i=1}^m \alpha_{x,i}^{(h)}\phi_i\).
See also
Other encoding functions:
compute_optimal_encoding(),
get_encoding(),
plotComponent(),
plotEigenvalues(),
predict.fmca(),
print.fmca(),
summary.fmca()
Examples
# Simulate the Jukes-Cantor model of nucleotide replacement
K <- 4
Tmax <- 6
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 = Tmax)
d_JK2 <- cut_data(d_JK, Tmax)
# create basis object
m <- 6
b <- create.bspline.basis(c(0, Tmax), nbasis = m, norder = 4)
# \donttest{
# compute encoding
encoding <- compute_optimal_encoding(d_JK2, b, computeCI = FALSE, nCores = 1)
#> ######### Compute encoding #########
#> Number of individuals: 10
#> Number of states: 4
#> Basis type: bspline
#> Number of basis functions: 6
#> Number of cores: 1
#>
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#>
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#> ---- Compute U matrix:
#>
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#>
#> DONE in 0.69s
#> ---- Compute encoding:
#> DONE in 0s
#> Run Time: 0.85s
# plot the encoding produced by the first harmonic
plot(encoding)
#> Warning: Removed 14 rows containing missing values (`geom_line()`).
# modify the plot using ggplot2
library(ggplot2)
plot(encoding, harm = 2, col = c("red", "blue", "darkgreen", "yellow")) +
labs(title = "Optimal encoding")
#> Warning: Removed 14 rows containing missing values (`geom_line()`).
# }