From c2e10054f61992f5e2a428f59f1976a738d8c84f Mon Sep 17 00:00:00 2001 From: Arnaud Duvermy <arnaud.duvermy@ens-lyon.fr> Date: Thu, 10 Feb 2022 16:58:48 +0100 Subject: [PATCH] Delete counts_matrix_generator.R --- src/counts_matrix_generator.R | 107 ---------------------------------- 1 file changed, 107 deletions(-) delete mode 100644 src/counts_matrix_generator.R diff --git a/src/counts_matrix_generator.R b/src/counts_matrix_generator.R deleted file mode 100644 index 2ca4417..0000000 --- a/src/counts_matrix_generator.R +++ /dev/null @@ -1,107 +0,0 @@ -############################# PCKGE REQUIRED ############################## -library(DESeq2) -library(ggplot2) -library(tydiverse) -### maybe others ### - - -# fix seed -set.seed(123) - - -## simulation functions -source("mydatalocal/counts_simulation/src/simulators.R") - - -#visualization function -source("mydatalocal/counts_simulation/src/visualization_fun.R") - - -########################## INPUT PARAMS ##################################### -N_cond = 2 -N_gene = 6000 -n_rep_sim = seq(2, 5, by = 1) ### number of replicate to assessed - - -############################ MU effect ####################################### - -mu_simul_dtf_res <- data.frame() -for (N_rep in n_rep_sim){ - mu_simul = seq(2500, 12000, by = 200) - #mu_simul - #mu_simul <- rep.int(1500, 8) - res_simul <- mu_effect(alpha = 2, mu_simul) - res_simul$N_rep <- N_rep - tmp_reshape_res_simul <- res_simul %>% reshape2::melt(.,id = c("vec_of_mu", "N_rep")) - mu_simul_dtf_res <- rbind(mu_simul_dtf_res, tmp_reshape_res_simul) -} - -###### LOG transform ####### - -# -> SEE linearity of var observed & mu - -#mu_simul_dtf_res$value[mu_simul_dtf_res$variable=="var_observ"]<-log(mu_simul_dtf_res$value[mu_simul_dtf_res$variable=="var_observ"]) -#mu_simul_dtf_res$vec_of_mu <- log(mu_simul_dtf_res$vec_of_mu) - -###### Visualization ###### -figure_mu_effect <- mu_effect_visualization(mu_simul_dtf_res) -figure_mu_effect - - -########################### ALPHA effect #################################### -n_rep_sim = seq(2, 5, by = 1) - -alpha_simul_dtf_res <- data.frame() -for (N_rep in n_rep_sim){ - alpha_simul = seq(0.01, 9, by = 0.1) - alpha_simul - #mu_simul <- rep.int(1500, 8) - res_simul <- size_effect(mu = 10000, size_simul) - res_simul$N_rep <- N_rep - tmp_reshape_res_simul <- res_simul %>% reshape2::melt(.,id = c("vec_of_alpha", "N_rep")) - alpha_simul_dtf_res <- rbind(alpha_simul_dtf_res, tmp_reshape_res_simul) -} - - -###### Visualization ###### -alpha_simul_dtf_res -figure_alpha_effect <- size_effect_visualization(alpha_simul_dtf_res) -figure_alpha_effect - - - -########################### EXPORT RESULTS ################################# - -svg("mydatalocal/counts_simulation/img/fig_mu_effect.svg") -figure_mu_effect -dev.off() - -svg("mydatalocal/counts_simulation/img/fig_size_effect.svg") -figure_alpha_effect -dev.off() - - - -########################### Beta test ##################################### - -## main -# Params to specify design -min_rep = 2 #/!\ = 1 forbidden -max_rep = 10 - - - -mu_simul = seq(100, 15000, by = 200) -mu_simul -mu_simul <- rep.int(1500, 8) -res_simul <- mu_effect(alpha = 2.9, mu_simul) -reshape_res_simul <- res_simul %>% reshape2::melt(.,id = c("vec_of_mu")) -mu_effect_visualization(reshape_res_simul) - - -alpha_simul = seq(0.01, 10, by = 0.1) -alpha_simul -res_simul2 <- size_effect(mu = 10000, alpha_simul) -res_simul2 -reshape_res_simul2 <- res_simul2 %>% reshape2::melt(.,id = c("vec_of_alpha")) -size_effect_visualization(reshape_res_simul2) -- GitLab