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added code to calculate time until better
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Eric Weine
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Mar 4, 2024
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,307 @@ | ||
| load("~/Documents/fastglmpca/inst/analysis/results.RData") | ||
|
|
||
| find_first_greater_index <- function(x, y) { | ||
| greater_indices <- which(y > x) | ||
| if (length(greater_indices) > 0) { | ||
| return(min(greater_indices)) | ||
| } else { | ||
| return(NA) | ||
| } | ||
| } | ||
|
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||
| K_vec <- c(2, 3, 4, 5, 10, 15, 25) | ||
|
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| time_until_beats_glmpca_1core <- c() | ||
| time_until_beats_glmpca_28core <- c() | ||
|
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| time_until_beats_scGBM_1core <- c() | ||
| time_until_beats_scGBM_28core <- c() | ||
|
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| for (K in K_vec) { | ||
|
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| ll_glmpca <- droplets_res_list$glmpca[[ | ||
| glue::glue("{K}_factors") | ||
| ]][["loglik"]] | ||
|
|
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| ll_scGBM <- droplets_res_list$scGBM[[ | ||
| glue::glue("{K}_factors") | ||
| ]][["loglik"]] | ||
|
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| best_ll_glmpca <- tail(ll_glmpca, 1) | ||
| best_ll_scGBM <- tail(ll_scGBM, 1) | ||
|
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| ll_fastglmpca_1core <- droplets_res_list$fastglmpca_1_core[[ | ||
| glue::glue("{K}_factors") | ||
| ]][["loglik"]] | ||
|
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||
| ll_fastglmpca_28cores <- droplets_res_list$fastglmpca_28_cores[[ | ||
| glue::glue("{K}_factors") | ||
| ]][["loglik"]] | ||
|
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||
| idx_1core_glmpca <- find_first_greater_index( | ||
| best_ll_glmpca, | ||
| ll_fastglmpca_1core | ||
| ) | ||
|
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||
| idx_28core_glmpca <- find_first_greater_index( | ||
| best_ll_glmpca, | ||
| ll_fastglmpca_28cores | ||
| ) | ||
|
|
||
| idx_1core_scGBM <- find_first_greater_index( | ||
| best_ll_scGBM, | ||
| ll_fastglmpca_1core | ||
| ) | ||
|
|
||
| idx_28core_scGBM <- find_first_greater_index( | ||
| best_ll_scGBM, | ||
| ll_fastglmpca_28cores | ||
| ) | ||
|
|
||
| if(is.na(idx_1core_glmpca)) { | ||
|
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| time_until_beats_glmpca_1core <- c( | ||
| time_until_beats_glmpca_1core, | ||
| Inf | ||
| ) | ||
|
|
||
| } else { | ||
|
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||
| time_until_beats_glmpca_1core <- c( | ||
| time_until_beats_glmpca_1core, | ||
| droplets_res_list$fastglmpca_1_core[[ | ||
| glue::glue("{K}_factors") | ||
| ]][["time"]][idx_1core_glmpca] / 3600 | ||
| ) | ||
|
|
||
| } | ||
|
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| if(is.na(idx_28core_glmpca)) { | ||
|
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| time_until_beats_glmpca_28core <- c( | ||
| time_until_beats_glmpca_28core, | ||
| Inf | ||
| ) | ||
|
|
||
| } else { | ||
|
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| time_until_beats_glmpca_28core <- c( | ||
| time_until_beats_glmpca_28core, | ||
| droplets_res_list$fastglmpca_28_cores[[ | ||
| glue::glue("{K}_factors") | ||
| ]][["time"]][idx_28core_glmpca] / 3600 | ||
| ) | ||
|
|
||
| } | ||
|
|
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| if(is.na(idx_1core_scGBM)) { | ||
|
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| time_until_beats_scGBM_1core <- c( | ||
| time_until_beats_scGBM_1core, | ||
| Inf | ||
| ) | ||
|
|
||
| } else { | ||
|
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||
| time_until_beats_scGBM_1core <- c( | ||
| time_until_beats_scGBM_1core, | ||
| droplets_res_list$fastglmpca_1_core[[ | ||
| glue::glue("{K}_factors") | ||
| ]][["time"]][idx_1core_scGBM] / 3600 | ||
| ) | ||
|
|
||
| } | ||
|
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| if(is.na(idx_28core_scGBM)) { | ||
|
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| time_until_beats_scGBM_28core <- c( | ||
| time_until_beats_scGBM_28core, | ||
| Inf | ||
| ) | ||
|
|
||
| } else { | ||
|
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| time_until_beats_scGBM_28core <- c( | ||
| time_until_beats_scGBM_28core, | ||
| droplets_res_list$fastglmpca_28_cores[[ | ||
| glue::glue("{K}_factors") | ||
| ]][["time"]][idx_28core_scGBM] / 3600 | ||
| ) | ||
|
|
||
| } | ||
|
|
||
| } | ||
|
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| df_droplets <- data.frame( | ||
| time_until_beats_glmpca_1core = time_until_beats_glmpca_1core, | ||
| time_until_beats_glmpca_28core = time_until_beats_glmpca_28core, | ||
| time_until_beats_scGBM_1core = time_until_beats_scGBM_1core, | ||
| time_until_beats_scGBM_28core = time_until_beats_scGBM_28core | ||
| ) | ||
|
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||
| library(dplyr) | ||
|
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||
| df_droplets <- df_droplets %>% | ||
| dplyr::mutate( | ||
| time_until_beats_glmpca_1core = if_else( | ||
| is.infinite(time_until_beats_glmpca_1core), | ||
| "> 10", | ||
| as.character(round(time_until_beats_glmpca_1core, 1)) | ||
| ), | ||
| time_until_beats_glmpca_28core = if_else( | ||
| is.infinite(time_until_beats_glmpca_28core), | ||
| "> 10", | ||
| as.character(round(time_until_beats_glmpca_28core, 2)) | ||
| ), | ||
| time_until_beats_scGBM_1core = as.character(round(time_until_beats_scGBM_1core, 2)), | ||
| time_until_beats_scGBM_28core = as.character(round(time_until_beats_scGBM_28core, 3)) | ||
| ) | ||
|
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| time_until_beats_glmpca_1core <- c() | ||
| time_until_beats_glmpca_28core <- c() | ||
|
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| time_until_beats_scGBM_1core <- c() | ||
| time_until_beats_scGBM_28core <- c() | ||
|
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| for (K in K_vec) { | ||
|
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| ll_glmpca <- pbmc_res_list$glmpca[[ | ||
| glue::glue("{K}_factors") | ||
| ]][["loglik"]] | ||
|
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||
| ll_scGBM <- pbmc_res_list$scGBM[[ | ||
| glue::glue("{K}_factors") | ||
| ]][["loglik"]] | ||
|
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| best_ll_glmpca <- tail(ll_glmpca, 1) | ||
| best_ll_scGBM <- tail(ll_scGBM, 1) | ||
|
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| ll_fastglmpca_1core <- pbmc_res_list$fastglmpca_1_core[[ | ||
| glue::glue("{K}_factors") | ||
| ]][["loglik"]] | ||
|
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||
| ll_fastglmpca_28cores <- pbmc_res_list$fastglmpca_28_cores[[ | ||
| glue::glue("{K}_factors") | ||
| ]][["loglik"]] | ||
|
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||
| idx_1core_glmpca <- find_first_greater_index( | ||
| best_ll_glmpca, | ||
| ll_fastglmpca_1core | ||
| ) | ||
|
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||
| idx_28core_glmpca <- find_first_greater_index( | ||
| best_ll_glmpca, | ||
| ll_fastglmpca_28cores | ||
| ) | ||
|
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| idx_1core_scGBM <- find_first_greater_index( | ||
| best_ll_scGBM, | ||
| ll_fastglmpca_1core | ||
| ) | ||
|
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| idx_28core_scGBM <- find_first_greater_index( | ||
| best_ll_scGBM, | ||
| ll_fastglmpca_28cores | ||
| ) | ||
|
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| if(is.na(idx_1core_glmpca)) { | ||
|
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| time_until_beats_glmpca_1core <- c( | ||
| time_until_beats_glmpca_1core, | ||
| Inf | ||
| ) | ||
|
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||
| } else { | ||
|
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| time_until_beats_glmpca_1core <- c( | ||
| time_until_beats_glmpca_1core, | ||
| pbmc_res_list$fastglmpca_1_core[[ | ||
| glue::glue("{K}_factors") | ||
| ]][["time"]][idx_1core_glmpca] / 3600 | ||
| ) | ||
|
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||
| } | ||
|
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| if(is.na(idx_28core_glmpca)) { | ||
|
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| time_until_beats_glmpca_28core <- c( | ||
| time_until_beats_glmpca_28core, | ||
| Inf | ||
| ) | ||
|
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||
| } else { | ||
|
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| time_until_beats_glmpca_28core <- c( | ||
| time_until_beats_glmpca_28core, | ||
| pbmc_res_list$fastglmpca_28_cores[[ | ||
| glue::glue("{K}_factors") | ||
| ]][["time"]][idx_28core_glmpca] / 3600 | ||
| ) | ||
|
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||
| } | ||
|
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| if(is.na(idx_1core_scGBM)) { | ||
|
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| time_until_beats_scGBM_1core <- c( | ||
| time_until_beats_scGBM_1core, | ||
| Inf | ||
| ) | ||
|
|
||
| } else { | ||
|
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| time_until_beats_scGBM_1core <- c( | ||
| time_until_beats_scGBM_1core, | ||
| pbmc_res_list$fastglmpca_1_core[[ | ||
| glue::glue("{K}_factors") | ||
| ]][["time"]][idx_1core_scGBM] / 3600 | ||
| ) | ||
|
|
||
| } | ||
|
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| if(is.na(idx_28core_scGBM)) { | ||
|
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| time_until_beats_scGBM_28core <- c( | ||
| time_until_beats_scGBM_28core, | ||
| Inf | ||
| ) | ||
|
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||
| } else { | ||
|
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| time_until_beats_scGBM_28core <- c( | ||
| time_until_beats_scGBM_28core, | ||
| pbmc_res_list$fastglmpca_28_cores[[ | ||
| glue::glue("{K}_factors") | ||
| ]][["time"]][idx_28core_scGBM] / 3600 | ||
| ) | ||
|
|
||
| } | ||
|
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| } | ||
|
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| df_pbmc <- data.frame( | ||
| time_until_beats_glmpca_1core = time_until_beats_glmpca_1core, | ||
| time_until_beats_glmpca_28core = time_until_beats_glmpca_28core, | ||
| time_until_beats_scGBM_1core = time_until_beats_scGBM_1core, | ||
| time_until_beats_scGBM_28core = time_until_beats_scGBM_28core | ||
| ) | ||
|
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| library(dplyr) | ||
|
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| df_pbmc <- df_pbmc %>% | ||
| dplyr::mutate( | ||
| time_until_beats_glmpca_1core = if_else( | ||
| is.infinite(time_until_beats_glmpca_1core), | ||
| "> 10", | ||
| as.character(round(time_until_beats_glmpca_1core, 1)) | ||
| ), | ||
| time_until_beats_glmpca_28core = if_else( | ||
| is.infinite(time_until_beats_glmpca_28core), | ||
| "> 10", | ||
| as.character(round(time_until_beats_glmpca_28core, 2)) | ||
| ), | ||
| time_until_beats_scGBM_1core = as.character(round(time_until_beats_scGBM_1core, 2)), | ||
| time_until_beats_scGBM_28core = as.character(round(time_until_beats_scGBM_28core, 3)) | ||
| ) | ||
|
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| rownames(df_pbmc) <- c("K = 2", "K = 3", "K = 4", "K = 5", "K = 10", "K = 15", "K = 25") | ||
| rownames(df_droplets) <- c("K = 2", "K = 3", "K = 4", "K = 5", "K = 10", "K = 15", "K = 25") |