plot.fmca {cfda} | R Documentation |
Plot the optimal encoding
Description
Plot the optimal encoding
Usage
## S3 method for class 'fmca'
plot(
x,
harm = 1,
states = NULL,
addCI = FALSE,
coeff = 1.96,
col = NULL,
nx = 128,
...
)
Arguments
x |
output of |
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 |
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 |
Details
The encoding for the harmonic h
is a_{x}^{(h)} \approx \sum_{i=1}^m \alpha_{x,i}^{(h)}\phi_i
.
Value
a ggplot
object that can be modified using ggplot2
package.
Author(s)
Quentin Grimonprez
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)
# compute encoding
encoding <- compute_optimal_encoding(d_JK2, b, computeCI = FALSE, nCores = 1)
# plot the encoding produced by the first harmonic
plot(encoding)
# modify the plot using ggplot2
library(ggplot2)
plot(encoding, harm = 2, col = c("red", "blue", "darkgreen", "yellow")) +
labs(title = "Optimal encoding")
[Package cfda version 0.11.0 Index]