add viber module #8797
add viber module #8797
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| library(VIBER) | ||
| library(dplyr) | ||
| library(tidyverse) |
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Your code calls tidyverse, but your conda library doesn't. If you actually need all of tidyverse, I think you need to add it to the conda environment yml.
| # Ensure the option vectors are length 2 (key/ value) to catch empty ones | ||
| args_vals = lapply(args_vals, function(z){ length(z) = 2; z}) | ||
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| parsed_args = structure(lapply(args_vals, function(x) x[2]), names = lapply(args_vals, function(x) x[1])) |
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This line seems an odd bit of code. Can you clarify what it does and why it is needed?
| output: | ||
| tuple val(meta), path("*_viber_best_st_fit.rds"), emit: viber_rds | ||
| tuple val(meta), path("*_viber_best_st_heuristic_fit.rds"), emit: viber_heuristic_rds | ||
| tuple val(meta), path("*_${plot1}"), emit: viber_plots_rds |
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I find this a bit weird that there are two options for outptut, but neither is actually optional.
Could you just use the common pattern as the defintion, like plot2 would be something like "heuristic.rds"
Why do you call them plots when they are rds (not plots)?
Don't plot1 and plo2 overlap with viber_rds and viber_heuristic_rds if you have more than one sample? If these are obligatory and always outputted, just make the other version optional.
| input_obj = readRDS("$rds_join") | ||
| if (class(input_obj) == "m_cnaqc") { | ||
| shared = input_obj %>% get_sample(sample=samples, which_obj="shared") | ||
| joint_table = lapply(names(shared), |
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I find the mixture of lapply and dplyr grating, and would prefer using purrr:: and dplyr::, but that's a personal taste.
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| ## Extract DP (depth) | ||
| dp = reads_data %>% | ||
| # dplyr::filter(mutation_id %in% non_tail) %>% ## this step should be managed before by other module |
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If these commented lines are not necessary, please just remove them.
| dp = reads_data %>% | ||
| # dplyr::filter(mutation_id %in% non_tail) %>% ## this step should be managed before by other module | ||
| dplyr::select(dplyr::starts_with("DP")) %>% | ||
| dplyr::mutate(dplyr::across(.cols=dplyr::everything(), |
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Wouldn't line 75 imply there is only one DP column? Then why eveything? Also, since the same code repeats, why not just use tidyr::replace_na() for all the values you want to replace in one go?
| #try(expr = {multivariate = plot(best_fit) %>% patchwork::wrap_plots()} ) | ||
| #top_p = patchwork::wrap_plots(marginals, multivariate, design=ifelse(n_samples>2, "ABB", "AAB")) | ||
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| try(expr = {multivariate = plot(best_fit)}) |
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There's no catch, so is the point only to continue if this fails? Or is the error standard? Do you need encapsulated in try? If not, just have the inside code and let it fail.
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| try(expr = {multivariate = plot(best_fit)}) | ||
| try(expr = {multivariate = ggpubr::ggarrange(plotlist = multivariate)}) | ||
| top_p = ggpubr::ggarrange(plotlist = list(marginals, multivariate), widths=ifelse(n_samples>2, c(1,2), c(2,1))) |
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Please try running a code fromatter, because these kind of lines are hard to read. RStudio has a good code formatter.
| @@ -0,0 +1,175 @@ | |||
| #!/usr/bin/env Rscript | |||
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I would prefer that the script be called something more informtive like
viber_main_script.R
or viber_template.R
or run_viber.R
Calling it main_script.R is too generic to be really useful.
PR checklist
Closes #8712
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda