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caravagnalab / revolver

REVOLVER - Repeated Evolution in Cancer
https://caravagnalab.github.io/revolver/
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Function define twice #15

Closed luca-dex closed 5 years ago

luca-dex commented 6 years ago

The function plot.rev_cohort_fit is defined twice. In lib_plot_fit.R and in rev_fit.R.

caravagn commented 6 years ago

Luca, can you check if they are the same definition and in case keep just one of the two?

luca-dex commented 6 years ago

They have different signatues, and different content:

In rev_fit.R:

plot.rev_cohort_fit = function(x,
    patients = x$patients,
    merge.files = FALSE,
    cex = 1)

In plot.rev_cohort_fit.R:

plot.rev_cohort_fit = function(x,
    patients = names(x$fit$phylogenies),
    plot.stat = TRUE,
    palette = 'Set1',
    out.file = 'REVOLVER-cohort.pdf',
    layout = paste(length(patients), 'x1', sep =''),
    alpha = 0.7,
    verbose = FALSE,
    ...
)
caravagn commented 5 years ago

I should have identified the most up to date implementation as the one in rev_fit.R. I commented out the other one and I can close this issue.