Plot reconstructed indicators
plotIndicatorsReconstruction(reconstruction, id, states = NULL)Arguments
- reconstruction
output of
reconstructIndicators- id
id of the individual to plot.
idmust be inreconstruction$id- states
states to plot, by default all states are plotted
Value
ggplot
See also
Examples
set.seed(42)
# Simulate the Jukes-Cantor model of nucleotide replacement
K <- 3
Tmax <- 1
d_JK <- generate_Markov(n = 100, K = K, Tmax = Tmax)
d_JK2 <- cut_data(d_JK, Tmax)
# create basis object
m <- 20
b <- create.bspline.basis(c(0, Tmax), nbasis = m, norder = 4)
# \donttest{
# compute encoding
encoding <- compute_optimal_encoding(d_JK2, b, computeCI = FALSE, nCores = 1)
#> ######### Compute encoding #########
#> Number of individuals: 100
#> Number of states: 3
#> Basis type: bspline
#> Number of basis functions: 20
#> Number of cores: 1
#> Method: precompute
#>
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#>
#> DONE in 0.51s
#> ---- Compute U matrix:
#>
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#>
#> DONE in 8.51s
#> ---- Compute encoding:
#> DONE in 0s
#> Run Time: 9.1s
indicators <- reconstructIndicators(encoding)
#> [1] "Reconstruct data using 37 components (out of 60)"
# we plot the first path and its reconstructed indicators
iInd <- 3
plotData(d_JK2[d_JK2$id == iInd, ])
plotIndicatorsReconstruction(indicators, id = iInd)
# the column state contains the state associated with the greatest indicator.
# So, the output can be used with plotData function
plotData(remove_duplicated_states(indicators[indicators$id == iInd, ]))
# }