A base callback function that returns a galgo.Obj

callback_base_return_pop (userdir = "",generation, pop_pool,
pareto, prob_matrix, current_time)

Arguments

userdir	the default directory used by `galgo()` to store files
generation	a number indicating the number of iterations of the galgo algorithm
pop_pool	a `data.frame` with the solution vectors, number of clusters and their ranking.
pareto	the solutions found by Galgo across all generations in the solution space
prob_matrix	a `matrix` or `data.frame`. Must be an expression matrix with features in rows and samples in columns
current_time	an `POSIXct` object

Value

an object of class galgo

Examples

# load example dataset

library(breastCancerTRANSBIG)
data(transbig)
Train <- transbig
rm(transbig)
#> Warning: object 'transbig' not found
expression <- Biobase::exprs(Train)
clinical <- Biobase::pData(Train)
OS <- survival::Surv(time = clinical$t.rfs, event = clinical$e.rfs)
# We will use a reduced dataset for the example
expression <- expression[sample(1:nrow(expression), 100), ]

# Now we scale the expression matrix
expression <- t(scale(t(expression)))

# Run galgo with base_return_pop_callback assigned to the end_galgo_callback
# hook-point
# By using this callback galgo() return a `galgo,Obj` object.
output <- GSgalgoR::galgo(generations = 5,
population = 15,
prob_matrix = expression,
OS = OS,
end_galgo_callback = callback_base_return_pop
)
#> Using CPU for computing pearson distance
#> Generation 1 Non-dominated solutions:
#>           k                      rnkIndex    CrowD
#> result.8  4 0.02559570 206.82540        1      Inf
#> result.10 4 0.05791995  14.48178        1      Inf
#> result.13 2 0.05073109  32.45238        1 1.313193
#> Generation 2 Non-dominated solutions:
#>           k                      rnkIndex     CrowD
#> result.1  6 0.03106352 210.57312        1       Inf
#> result.3  2 0.07486536  45.95706        1       Inf
#> result.13 4 0.05948496  95.64288        1 0.8823692
#> result.10 4 0.06508901  94.40352        1 0.3849673
#> Generation 3 Non-dominated solutions:
#>          k                      rnkIndex     CrowD
#> result.1 6 0.03106352 210.57312        1       Inf
#> result.3 2 0.07486536  45.95706        1       Inf
#>          4 0.05252796 162.56503        1 0.8986327
#>          3 0.07290575 130.81743        1 0.8572644
#> Generation 4 Non-dominated solutions:
#>           k                       rnkIndex     CrowD
#>          10 -0.00671469 306.82977        1       Inf
#>           3  0.08651116  16.38125        1       Inf
#> result.1  6  0.03106352 210.57312        1 1.1094377
#>           4  0.05252796 162.56503        1 0.7108536
#>           3  0.07290575 130.81743        1 0.5564300
#>           3  0.08101525  86.20927        1 0.5219056
#> Generation 5 Non-dominated solutions:
#>   k                       rnkIndex     CrowD
#>  10 -0.00671469 306.82977        1       Inf
#>   3  0.08651116  16.38125        1       Inf
#>   5  0.03436379 245.48002        1 1.1083379
#>   4  0.05252796 162.56503        1 0.7892608
#>   3  0.07290575 130.81743        1 0.5558479
#>   3  0.08101525  86.20927        1 0.5210333