diff --git a/src/main.R b/src/main.R new file mode 100644 index 0000000000000000000000000000000000000000..1277089a84bd5f3cda2d3c3aab1a122034b7ac28 --- /dev/null +++ b/src/main.R @@ -0,0 +1,111 @@ +############################# PCKGE REQUIRED ############################## +library(DESeq2) +library(ggplot2) +library(tydiverse) +### maybe others ### + + +########################## change your home path ########################## +setwd("mydatalocal/counts_simulation/src") + +# fix seed +set.seed(123) + + + +########################## IMPORT FUN ############################### +## simulation functions +source("simulators.R") + + +#visualization function +source("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$vec_of_mu) + + +###### Visualization ###### +figure_mu_effect <- mu_effect_visualization(mu_simul_dtf_res) +figure_mu_effect + + +########################### ALPHA effect #################################### +n_rep_sim = seq(2, 5, by = 1) + +alpha_simul_dtf_res <- data.frame() +for (N_rep in n_rep_sim){ + alpha_simul = seq(0.2, 7, by = 0.2) + alpha_simul + res_simul <- size_effect(mu = 10000, alpha_simul) + res_simul$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)