update src count_matrix_genrator

src/counts_matrix_generator.R

@@ -8,14 +8,18 @@ source("mydatalocal/counts_simulation/src/simulators.R")
 
 # visualization functions
 mu_effect_visualization <- function(mu_effect_res){
+  label_wrap <- c("mu observed", "N gene DE", "min(|logFC|)", "var observed")
+  names(label_wrap) <- c("mu_observ", "res_DEA", "statistical_power", "var_observ")
   figure = mu_effect_res %>% ggplot(., aes(x=vec_of_mu, y = value, col=factor(N_rep))) +
-     geom_point() + facet_wrap(~variable, scales = "free_y")  
+     geom_point() + facet_wrap(~variable, scales = "free_y", labeller = labeller(variable = label_wrap))  + labs(color = "N replicates")
   return(figure)
 }
 
 size_effect_visualization <- function(alpha_effect_res){
-  figure = alpha_effect_res %>% ggplot(., aes(x=vec_of_alpha, y = value, na.rm = TRUE)) +
-    geom_point() + facet_wrap(~variable, scales = "free_y")
+  label_wrap <- c("mu observed", "N gene DE", "min(|logFC|)", "var observed")
+  names(label_wrap) <- c("mu_observ", "res_DEA", "statistical_power", "var_observ")
+  figure = alpha_effect_res %>% ggplot(., aes(x=vec_of_alpha, y = value, col=factor(N_rep))) +
+    geom_point() + facet_wrap(~variable, scales = "free_y", labeller = labeller(variable = label_wrap))  + labs(color = "N replicates")
   return(figure)
 }
 
@@ -57,10 +61,35 @@ for (N_rep in n_rep_sim){
   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)
 }
-mu_simul_dtf_res
-mu_effect_visualization(mu_simul_dtf_res)
 
+## LOG transform
+#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
+svg("mydatalocal/counts_simulation/img/fig_mu_effect.svg")
+figure_mu_effect
+dev.off()
+
+########################### ALPHA effect ####################################
+n_rep_sim = seq(2, 5, by = 1)
+
+alpha_simul_dtf_res <- data.frame()
 for (N_rep in n_rep_sim){
-  print(N_rep)
+  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)
 }
+alpha_simul_dtf_res
+figure_alpha_effect <- size_effect_visualization(alpha_simul_dtf_res)
+
+svg("mydatalocal/counts_simulation/img/fig_size_effect.svg")
+figure_alpha_effect
+dev.off()