Delete main.R

src/main.R

-############################# 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 #####################################
-