Multivariate Bayesian variable selection regression

Purity result summary

Result of this notebook has been uploaded here.

In [1]:
%cd ~/GIT/github/mvarbvs/dsc

/home/gaow/GIT/github/mvarbvs/dsc
In [2]:
plots = dscrutils::dscquery('benchmark', 
                    target = "liter_data.dataset simple_lm.pve simple_lm.n_signal simple_lm fit_susie.estimate_residual_variance fit_susie.prior_var plot_sse plot_susie")

Loading dsc-query output from CSV file.
In [4]:
head(plots)
DSCliter_data.datasetsimple_lm.n_signalsimple_lm.output.filesimple_lm.pvefit_susie.estimate_residual_variancefit_susie.prior_varplot_sse.output.fileplot_susie.output.file
1 ~/Documents/GTExV8/Thyroid.Lung.FMO2.filled.rds 1 simple_lm/liter_data_1_summarize_ld_1_simple_lm_1 0.05 FALSE 0.05 plot_sse/liter_data_1_summarize_ld_1_simple_lm_1_fit_susie_1_plot_sse_1 plot_susie/liter_data_1_summarize_ld_1_simple_lm_1_fit_susie_1_plot_susie_1
1 ~/Documents/GTExV8/Thyroid.Lung.FMO2.filled.rds 1 simple_lm/liter_data_1_summarize_ld_1_simple_lm_1 0.05 FALSE 0.10 plot_sse/liter_data_1_summarize_ld_1_simple_lm_1_fit_susie_3_plot_sse_1 plot_susie/liter_data_1_summarize_ld_1_simple_lm_1_fit_susie_3_plot_susie_1
1 ~/Documents/GTExV8/Thyroid.Lung.FMO2.filled.rds 1 simple_lm/liter_data_1_summarize_ld_1_simple_lm_1 0.05 FALSE 0.20 plot_sse/liter_data_1_summarize_ld_1_simple_lm_1_fit_susie_5_plot_sse_1 plot_susie/liter_data_1_summarize_ld_1_simple_lm_1_fit_susie_5_plot_susie_1
1 ~/Documents/GTExV8/Thyroid.Lung.FMO2.filled.rds 1 simple_lm/liter_data_1_summarize_ld_1_simple_lm_1 0.05 FALSE 0.40 plot_sse/liter_data_1_summarize_ld_1_simple_lm_1_fit_susie_7_plot_sse_1 plot_susie/liter_data_1_summarize_ld_1_simple_lm_1_fit_susie_7_plot_susie_1
1 ~/Documents/GTExV8/Thyroid.Lung.FMO2.filled.rds 1 simple_lm/liter_data_1_summarize_ld_1_simple_lm_1 0.05 TRUE 0.05 plot_sse/liter_data_1_summarize_ld_1_simple_lm_1_fit_susie_2_plot_sse_1 plot_susie/liter_data_1_summarize_ld_1_simple_lm_1_fit_susie_2_plot_susie_1
1 ~/Documents/GTExV8/Thyroid.Lung.FMO2.filled.rds 1 simple_lm/liter_data_1_summarize_ld_1_simple_lm_1 0.05 TRUE 0.10 plot_sse/liter_data_1_summarize_ld_1_simple_lm_1_fit_susie_4_plot_sse_1 plot_susie/liter_data_1_summarize_ld_1_simple_lm_1_fit_susie_4_plot_susie_1
In [10]:
%get plots --from R
In [7]:
plots.columns
Out[7]:
Index(['DSC', 'liter_data.dataset', 'simple_lm.n_signal',
       'simple_lm.output.file', 'simple_lm.pve',
       'fit_susie.estimate_residual_variance', 'fit_susie.prior_var',
       'plot_sse.output.file', 'plot_susie.output.file'],
      dtype='object')
In [14]:
plots['simple_lm.output.file'] = plots['simple_lm.output.file'].astype(str) + '.cache.sim.1.png'
plots['plot_sse.output.file'] = plots['plot_sse.output.file'].astype(str) + '.plot_file.1.png'
plots['plot_susie.output.file'] = plots['plot_susie.output.file'].astype(str) + '.seg.1.png'
In [ ]:
rename = {}
for k in plots.columns:
    kk = k.split('.',1)
    if len(kk) == 1:
        continue
    if kk[1] == 'output.file':
        rename[k] = kk[0]
    else:
        rename[k] = kk[1]
In [30]:
plots.rename(columns=rename).drop(columns=['DSC']).to_csv("benchmark/susie_dsc.csv", index=False)

Pack for distribute

In [32]:
cd benchmark && mkdir susie_dsc && cp simple_lm/*.png plot_sse/*.png plot_susie/*.png susie_dsc.csv susie_dsc && cd susie_dsc && dsc-io susie_dsc.csv index.html
Copyright © 2016-2020 Gao Wang et al at Stephens Lab, University of Chicago