R/callback-functions.R
callback_no_report.RdThe main idea behind this callback function is to provide some feedback to the user about galgo execution. No other relevant information is shown
callback_no_report (userdir = "",generation, pop_pool, pareto, prob_matrix, current_time)
| 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 |
| pareto | the solutions found by Galgo across all generations in the solution space |
| prob_matrix | a |
| current_time | an |
Nothing.
#> Warning: object 'transbig' not foundexpression <- 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 no_report_callback assigned to the report_callback # hook-point GSgalgoR::galgo(generations = 5, population = 15, prob_matrix = expression, OS = OS, report_callback = callback_no_report )#>#> ....*#> An object of class "galgo.Obj" #> Slot "Solutions": #> 208276_at 211240_x_at 201006_at 209307_at 215845_x_at 201596_x_at #> result.15 1 1 0 1 1 0 #> 0 1 0 0 1 1 #> 0 1 0 0 1 1 #> result.3 0 1 0 0 1 1 #> result.9 0 0 0 0 1 0 #> 1 1 0 1 1 0 #> 0 1 0 1 1 1 #> 1 1 1 1 1 0 #> result.13 1 1 1 1 1 1 #> 0 1 0 0 1 1 #> result.14 1 1 0 0 1 1 #> result.9 0 0 0 1 0 0 #> 1 1 0 1 1 0 #> 1 1 0 1 1 0 #> 1 0 1 1 1 1 #> 214612_x_at 210727_at 208829_at 212199_at 211513_s_at 207804_s_at #> result.15 0 1 1 1 1 1 #> 1 0 0 1 0 1 #> 1 0 0 0 1 1 #> result.3 1 0 0 1 0 1 #> result.9 1 1 0 0 0 0 #> 1 1 1 1 1 1 #> 1 1 1 1 1 0 #> 1 0 0 1 0 1 #> result.13 1 0 0 0 1 1 #> 1 0 0 1 0 1 #> result.14 1 0 0 1 0 1 #> result.9 0 0 0 0 0 1 #> 0 1 1 1 1 1 #> 1 0 1 1 1 1 #> 1 0 0 0 1 1 #> 216266_s_at 221768_at 203597_s_at 216830_at 208231_at 206201_s_at #> result.15 1 1 1 0 0 1 #> 0 0 1 0 1 1 #> 0 0 1 0 1 1 #> result.3 0 0 1 0 1 1 #> result.9 0 0 1 1 1 0 #> 1 1 1 0 0 1 #> 0 0 1 0 1 1 #> 0 1 1 1 1 1 #> result.13 0 0 1 0 1 1 #> 0 0 1 0 1 1 #> result.14 0 0 1 0 1 1 #> result.9 0 0 0 1 0 0 #> 1 1 1 0 0 1 #> 1 1 1 0 0 1 #> 0 0 1 0 1 1 #> 205317_s_at 218268_at 208994_s_at 204449_at 201712_s_at 221433_at #> result.15 1 1 1 1 1 1 #> 1 1 1 0 0 1 #> 1 1 1 0 0 1 #> result.3 1 1 1 0 0 1 #> result.9 1 0 1 0 0 1 #> 1 1 1 1 1 1 #> 1 1 1 0 1 1 #> 1 1 1 0 0 1 #> result.13 1 1 1 1 0 1 #> 1 1 1 0 0 1 #> result.14 1 1 1 0 0 1 #> result.9 0 0 0 0 1 0 #> 1 1 1 1 1 1 #> 1 1 1 1 1 1 #> 1 1 1 1 0 1 #> 218767_at 221789_x_at 204231_s_at 218834_s_at 204282_s_at 213638_at #> result.15 1 0 0 1 0 1 #> 0 0 1 0 1 1 #> 1 0 1 1 1 1 #> result.3 0 1 1 0 1 1 #> result.9 1 0 1 1 1 0 #> 1 0 0 0 1 1 #> 1 0 1 0 1 1 #> 0 1 1 1 1 1 #> result.13 1 1 1 0 1 1 #> 0 1 1 0 1 1 #> result.14 0 1 1 0 1 1 #> result.9 0 0 0 0 0 0 #> 1 0 0 1 0 1 #> 1 1 0 1 0 1 #> 1 1 1 1 1 1 #> 202707_at 201810_s_at 211095_at 203764_at 219582_at 214583_at #> result.15 1 0 0 1 1 0 #> 0 0 1 1 0 1 #> 0 0 1 1 0 0 #> result.3 0 0 0 0 0 1 #> result.9 1 0 0 0 1 0 #> 1 0 0 1 1 1 #> 0 1 1 1 0 1 #> 0 1 1 1 0 1 #> result.13 0 0 1 1 0 1 #> 0 0 0 0 0 0 #> result.14 0 0 0 1 0 1 #> result.9 0 1 0 0 0 0 #> 1 0 0 1 0 0 #> 1 0 1 1 1 0 #> 0 0 1 1 0 0 #> 220170_at 206058_at 207432_at 220490_at 202572_s_at 203548_s_at #> result.15 1 0 1 1 1 1 #> 1 1 0 1 1 0 #> 1 1 0 1 1 0 #> result.3 1 1 0 1 1 0 #> result.9 1 0 1 0 0 1 #> 1 1 1 1 1 0 #> 1 1 0 1 1 0 #> 1 1 1 1 1 0 #> result.13 1 1 0 1 1 0 #> 1 1 0 1 1 0 #> result.14 1 1 0 1 1 0 #> result.9 0 1 0 0 0 0 #> 1 0 1 1 1 1 #> 1 1 1 1 1 1 #> 1 1 0 1 1 0 #> 220496_at 212691_at 206111_at 206765_at 217469_at 202228_s_at #> result.15 1 1 1 1 1 1 #> 1 0 1 1 0 0 #> 1 0 1 0 1 0 #> result.3 1 0 1 1 0 0 #> result.9 1 0 0 0 1 0 #> 1 1 1 1 0 1 #> 1 0 1 1 1 0 #> 0 1 1 1 1 0 #> result.13 1 0 1 1 1 0 #> 1 0 1 1 0 0 #> result.14 0 0 1 1 0 0 #> result.9 0 0 0 0 0 0 #> 1 1 1 1 1 1 #> 1 1 0 1 1 1 #> 1 0 1 1 1 0 #> 210247_at 214943_s_at 218941_at 201373_at 202009_at 213335_s_at #> result.15 1 1 0 1 1 1 #> 0 0 1 1 0 1 #> 0 1 1 1 0 1 #> result.3 0 0 0 1 0 0 #> result.9 0 0 0 1 1 1 #> 1 1 0 1 1 1 #> 0 1 1 1 1 1 #> 1 0 1 1 1 1 #> result.13 1 1 1 1 0 1 #> 0 0 0 1 0 0 #> result.14 1 0 1 1 0 0 #> result.9 0 0 0 0 0 0 #> 1 1 0 1 1 1 #> 1 1 0 1 1 1 #> 1 1 1 1 0 1 #> 206921_at 206564_at 212059_s_at 216443_at 219662_at 1007_s_at #> result.15 1 1 1 1 1 1 #> 1 1 1 1 1 0 #> 1 0 0 1 1 0 #> result.3 1 1 1 0 1 0 #> result.9 1 0 0 1 0 1 #> 1 1 1 0 1 1 #> 1 1 1 1 1 0 #> 1 1 1 1 1 0 #> result.13 1 1 0 0 1 1 #> 1 1 1 0 1 0 #> result.14 1 1 1 0 1 0 #> result.9 0 1 0 0 0 0 #> 1 1 1 1 1 1 #> 1 1 1 1 1 1 #> 1 0 0 0 1 1 #> 213621_s_at 202481_at 221217_s_at 203260_at 215428_at 220867_s_at #> result.15 1 1 1 1 1 1 #> 0 1 0 1 0 1 #> 0 1 0 1 0 1 #> result.3 0 1 0 1 0 0 #> result.9 1 0 0 1 0 0 #> 1 1 1 1 1 1 #> 0 1 0 1 0 1 #> 1 1 0 0 1 1 #> result.13 0 1 0 1 0 1 #> 0 1 0 1 0 0 #> result.14 0 1 0 1 0 0 #> result.9 0 1 0 1 0 0 #> 1 1 1 1 1 1 #> 1 1 1 1 1 0 #> 0 1 0 1 0 1 #> 211426_x_at 221658_s_at AFFX-HUMRGE/M10098_3_at 212019_at 213500_at #> result.15 1 0 1 1 1 #> 0 0 1 1 0 #> 0 1 1 1 0 #> result.3 0 1 1 1 0 #> result.9 1 1 1 1 0 #> 0 0 1 1 0 #> 0 1 1 1 1 #> 0 1 1 1 1 #> result.13 0 1 0 1 0 #> 0 1 1 1 0 #> result.14 0 1 1 1 0 #> result.9 0 0 0 0 0 #> 1 0 1 1 1 #> 1 0 1 1 1 #> 0 1 0 1 0 #> 221259_s_at 215012_at 207535_s_at 202118_s_at 204625_s_at 206540_at #> result.15 1 1 1 1 0 1 #> 1 1 1 1 0 0 #> 1 1 1 1 0 1 #> result.3 0 1 1 1 0 0 #> result.9 1 1 0 0 1 0 #> 0 1 1 1 0 0 #> 1 1 1 1 0 1 #> 1 1 1 1 1 0 #> result.13 1 1 1 1 0 1 #> 1 1 1 1 0 0 #> result.14 0 0 1 1 0 0 #> result.9 0 0 0 0 0 0 #> 1 1 1 1 0 1 #> 1 1 1 1 0 1 #> 1 1 1 1 0 1 #> 214608_s_at 203682_s_at 206203_at 200753_x_at 202518_at 207936_x_at #> result.15 1 1 0 1 1 1 #> 0 1 1 0 1 0 #> 0 1 1 1 1 0 #> result.3 1 1 1 0 1 0 #> result.9 0 0 0 1 1 0 #> 1 1 0 0 1 1 #> 0 1 1 1 1 1 #> 1 1 1 0 1 0 #> result.13 1 1 1 1 1 0 #> 1 1 1 0 1 0 #> result.14 1 1 1 0 1 0 #> result.9 0 0 0 0 0 0 #> 1 1 0 1 1 1 #> 1 1 0 1 1 1 #> 0 1 1 1 1 0 #> 215183_at 208069_x_at 204159_at 213965_s_at 221617_at 216958_s_at #> result.15 1 1 1 0 1 1 #> 1 0 0 0 1 1 #> 1 1 0 0 1 1 #> result.3 1 0 0 0 1 1 #> result.9 1 1 1 0 1 0 #> 1 1 0 0 1 1 #> 1 1 0 0 1 0 #> 0 0 0 1 1 1 #> result.13 1 1 0 0 1 1 #> 1 0 0 0 1 1 #> result.14 1 0 0 0 1 1 #> result.9 0 1 0 0 0 1 #> 1 1 1 0 1 1 #> 1 1 1 0 1 1 #> 1 1 0 0 1 1 #> 215762_at 214682_at 213605_s_at 212229_s_at 203492_x_at 218824_at #> result.15 0 1 1 1 0 1 #> 0 0 1 1 1 1 #> 0 0 1 1 1 1 #> result.3 1 0 1 1 1 1 #> result.9 0 0 0 0 1 0 #> 0 0 1 1 1 1 #> 1 0 1 1 1 1 #> 1 0 0 1 1 1 #> result.13 1 0 0 1 1 1 #> 1 0 1 1 1 1 #> result.14 1 0 0 1 1 1 #> result.9 0 0 0 1 0 0 #> 0 1 1 1 0 1 #> 1 1 1 1 0 1 #> 1 0 0 1 1 1 #> 220812_s_at 210872_x_at 213922_at 214159_at 209535_s_at k #> result.15 1 1 1 1 1 7 #> 1 1 0 0 1 2 #> 1 1 0 0 1 5 #> result.3 1 1 0 0 1 2 #> result.9 1 0 0 1 0 10 #> 1 1 1 1 1 6 #> 1 1 0 0 1 2 #> 1 1 1 1 1 2 #> result.13 1 1 1 0 1 2 #> 1 1 0 0 1 2 #> result.14 1 1 0 0 1 2 #> result.9 0 0 0 0 0 2 #> 1 0 1 1 1 7 #> 1 1 1 1 1 7 #> 1 1 1 0 1 5 #> rnkIndex CrowD #> result.15 0.02431213 262.79073 1 Inf #> 0.09865128 230.56927 1 Inf #> 0.03678756 252.92541 1 0.7816078 #> result.3 0.09704814 91.66167 2 Inf #> result.9 -0.01429944 238.74222 2 Inf #> 0.03088650 237.73015 2 0.7875784 #> 0.05287022 188.39536 2 0.5683238 #> 0.05556335 146.41825 2 0.4869773 #> result.13 0.08385136 132.88299 2 0.4031756 #> 0.09277432 127.17414 2 0.1793662 #> result.14 0.09667224 115.69393 2 0.1738992 #> result.9 0.09036216 58.64087 3 Inf #> 0.01611480 215.25780 3 Inf #> 0.02984614 213.94958 3 0.4159988 #> 0.03778117 156.74672 3 0.4073372 #> #> Slot "ParetoFront": #> [[1]] #> [,1] [,2] #> result.1 0.044079314 71.19605 #> result.2 0.026139667 17.30654 #> result.3 0.012209631 111.77052 #> result.4 0.021754619 118.08292 #> result.5 0.006081003 40.16175 #> result.6 0.036979925 148.63547 #> result.7 0.048008684 42.93976 #> result.8 0.033147918 75.26986 #> result.9 0.090362158 58.64087 #> result.10 0.021572026 84.70667 #> result.11 -0.014222997 112.22295 #> result.12 0.018121489 5.86589 #> result.13 0.015541257 94.55781 #> result.14 0.096672242 115.69393 #> #> [[2]] #> #> result.3 0.0970481380 91.66167 #> result.15 0.0243121338 262.79073 #> result.6 0.0369799250 148.63547 #> result.13 0.0838513642 132.88299 #> result.14 0.0966722422 115.69393 #> result.9 0.0903621580 58.64087 #> result.9 -0.0142994429 238.74222 #> result.1 0.0691510166 129.91117 #> result.6 0.0134643264 209.73971 #> result.7 0.0480086837 42.93976 #> result.8 0.0001009192 149.45557 #> result.1 0.0440793139 71.19605 #> result.10 0.0086043263 130.42500 #> result.4 0.0217546192 118.08292 #> result.12 0.0345737519 102.28249 #> #> [[3]] #> #> result.3 0.0970481380 91.66167 #> result.15 0.0243121338 262.79073 #> result.6 0.0369799250 148.63547 #> result.13 0.0838513642 132.88299 #> 0.0367875605 252.92541 #> result.14 0.0966722422 115.69393 #> result.9 0.0903621580 58.64087 #> result.9 -0.0142994429 238.74222 #> result.1 0.0691510166 129.91117 #> 0.0429419377 132.25239 #> result.6 0.0134643264 209.73971 #> 0.0223463738 156.12843 #> 0.0141982901 180.76370 #> result.8 0.0001009192 149.45557 #> 0.0585861250 60.70461 #> #> [[4]] #> #> result.3 0.09704814 91.66167 #> result.15 0.02431213 262.79073 #> result.6 0.03697993 148.63547 #> 0.03678756 252.92541 #> result.13 0.08385136 132.88299 #> 0.05556335 146.41825 #> result.14 0.09667224 115.69393 #> result.9 0.09036216 58.64087 #> result.9 -0.01429944 238.74222 #> result.1 0.06915102 129.91117 #> result.6 0.01346433 209.73971 #> 0.02234637 156.12843 #> 0.01419829 180.76370 #> 0.04052784 132.31614 #> 0.04294194 132.25239 #> #> [[5]] #> #> result.15 0.02431213 262.79073 #> 0.09865128 230.56927 #> 0.03678756 252.92541 #> result.3 0.09704814 91.66167 #> result.9 -0.01429944 238.74222 #> 0.03088650 237.73015 #> 0.05287022 188.39536 #> 0.05556335 146.41825 #> result.13 0.08385136 132.88299 #> 0.09277432 127.17414 #> result.14 0.09667224 115.69393 #> result.9 0.09036216 58.64087 #> 0.01611480 215.25780 #> 0.02984614 213.94958 #> 0.03778117 156.74672 #> #>