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AJResearchGroup / nsphs_ml_qt

R package for nsphs_ml_qt
GNU General Public License v3.0
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Always plot the distribution of the phenotype input data #33

Closed richelbilderbeek closed 2 years ago

richelbilderbeek commented 2 years ago

I want a histogram and box plot of the phenotypic data

richelbilderbeek commented 2 years ago

These are the plots:

trait_value_box_plot trait_value_density_plot trait_value_histogram

richelbilderbeek commented 2 years ago

Works locally:

richel@N141CU:~/GitHubs$ cd ~/sim_data_issue_18_ae/
richel@N141CU:~/sim_data_issue_18_ae$ ls
ae.M1.ex3.b_0_4.sim_data_issue_18.p0  losses_from_train_v.png    score_per_pop.csv  train_times.png
genotype_concordances.csv             nmse_in_time.csv           score_per_pop.png  trait_value_box_plot.png
losses_from_train_t.csv               nmse_in_time.png           scores.csv         trait_value_density_plot.png
losses_from_train_t.png               phenotype_predictions.csv  scores.png         trait_value_histogram.png
losses_from_train_v.csv               phenotype_predictions.png  train_times.csv
richelbilderbeek commented 2 years ago

There is this problem though:

Starting time: 2022-05-04T15:15:27+02:00
Running on computer with HOSTNAME: N141CU
Running at location /home/richel/GitHubs
'nsphs_ml_qt.sif' running with arguments 'Rscript nsphs_ml_qt/scripts_rackham/25_run.R /home/richel/sim_data_issue_18/experiment_params.csv'
gcae_experiment_params_filename: /home/richel/sim_data_issue_18/experiment_params.csv
Running the GCAE experiment
Error: nrow(losses_from_project_table) not equal to length(gcae_experiment_params$analyse_epochs).
1/1 mismatches
[1] 14 - 10 == 4
Execution halted
End time: 2022-05-04T15:30:47+02:00
Duration: 920 seconds
Parameters: /home/richel/sim_data_issue_18/experiment_params.csv
Number of parameters: 1
Correct number of arguments: 1
Starting time: 2022-05-04T15:30:47+02:00
Running on computer with HOSTNAME: N141CU
Running at location /home/richel/GitHubs
gcae_experiment_params_filename: /home/richel/sim_data_issue_18/experiment_params.csv
singularity_filename: nsphs_ml_qt/nsphs_ml_qt.sif
unique_id: issue_18
datadir: /home/richel/sim_data_issue_18/
trainedmodeldir: ~/sim_data_issue_18_ae/
zip_filename: /home/richel/issue_18.zip
log_filenames: 
datadir_basename: sim_data_issue_18
trainedmodeldir_basename: sim_data_issue_18_ae
    zip warning: name not matched: sim_data_issue_18
    zip warning: name not matched: sim_data_issue_18_ae

zip error: Nothing to do! (/home/richel/issue_18.zip)
End time: 2022-05-04T15:30:49+02:00
Duration: 2 seconds
End time: 2022-05-04T15:30:49+02:00
Duration: 932 seconds
richelbilderbeek commented 2 years ago

Maybe running from the absolute start fixes it...

richel@N141CU:~$ ls
codeberg               Downloads                hello     processing             script_checker        Templates
data_issue_5           Emulation                Music     Project_1_SciRep_2019  sim_data_issue_18     Videos
data_richel_issue_129  gcae_input_files_1_ae    notes     Public                 sim_data_issue_18_ae
Desktop                git_for_young_teenagers  out_ae    R                      sketchbook
Documents              GitHubs                  Pictures  requirements.txt       snap
richel@N141CU:~$ rm -rf sim_data_issue_18
richel@N141CU:~$ rm -rf sim_data_issue_18_ae/
richelbilderbeek commented 2 years ago

Works!

Running the GCAE experiment
Save the GCAE experiment results
$genotype_concordances_filename
[1] "~/sim_data_issue_18_ae//genotype_concordances.csv"

$losses_from_train_t_filename
[1] "~/sim_data_issue_18_ae//losses_from_train_t.csv"

$losses_from_train_v_filename
[1] "~/sim_data_issue_18_ae//losses_from_train_v.csv"

$nmse_in_time_filename
[1] "~/sim_data_issue_18_ae//nmse_in_time.csv"

$phenotype_predictions_filename
[1] "~/sim_data_issue_18_ae//phenotype_predictions.csv"

$scores_filename
[1] "~/sim_data_issue_18_ae//scores.csv"

$score_per_pop_filename
[1] "~/sim_data_issue_18_ae//score_per_pop.csv"

$train_times_filename
[1] "~/sim_data_issue_18_ae//train_times.csv"

Create the GCAE experiment results' plots
$genotype_concordances_filename
[1] "~/sim_data_issue_18_ae//genotype_concordances.png"

$losses_from_train_t_filename
[1] "~/sim_data_issue_18_ae//losses_from_train_t.png"

$losses_from_train_v_filename
[1] "~/sim_data_issue_18_ae//losses_from_train_v.png"

$nmse_in_time_filename
[1] "~/sim_data_issue_18_ae//nmse_in_time.png"

$phenotype_predictions_filename
[1] "~/sim_data_issue_18_ae//phenotype_predictions.png"

$scores_filename
[1] "~/sim_data_issue_18_ae//scores.png"

$score_per_pop_filename
[1] "~/sim_data_issue_18_ae//score_per_pop.png"

$train_times_filename
[1] "~/sim_data_issue_18_ae//train_times.png"

Warning message:
In grSoftVersion() :
  unable to load shared object '/usr/local/lib/R/modules//R_X11.so':
  libXt.so.6: cannot open shared object file: No such file or directory
End time: 2022-05-04T15:55:01+02:00
Duration: 843 seconds
Parameters: /home/richel/sim_data_issue_18/experiment_params.csv
Number of parameters: 1
Correct number of arguments: 1
Starting time: 2022-05-04T15:55:01+02:00
Running on computer with HOSTNAME: N141CU
Running at location /home/richel/GitHubs
gcae_experiment_params_filename: /home/richel/sim_data_issue_18/experiment_params.csv
singularity_filename: nsphs_ml_qt/nsphs_ml_qt.sif
unique_id: issue_18
datadir: /home/richel/sim_data_issue_18/
trainedmodeldir: ~/sim_data_issue_18_ae/
zip_filename: /home/richel/issue_18.zip
log_filenames: 
datadir_basename: sim_data_issue_18
trainedmodeldir_basename: sim_data_issue_18_ae
    zip warning: name not matched: sim_data_issue_18
    zip warning: name not matched: sim_data_issue_18_ae

zip error: Nothing to do! (/home/richel/issue_18.zip)
End time: 2022-05-04T15:55:02+02:00
Duration: 1 seconds
End time: 2022-05-04T15:55:02+02:00
Duration: 854 seconds
richelbilderbeek commented 2 years ago

(sure, the zipping is not important now)