benchmark with default values changed

Merge branch 'master' of https://github.com/hadexversum/HRaDeX # Conflicts: # inst/benchmark.R
hadexversum · Aug 13, 2024 · 19c4102 · 19c4102
2 parents 552ff69 + acc05c5
commit 19c4102
Showing 1 changed file with 12 additions and 8 deletions.
diff --git a/inst/benchmark.R b/inst/benchmark.R
@@ -1,4 +1,7 @@
 library(patchwork)
+library(ggplot2)
+library(dplyr)
+library(HRaDeX)
 
 calculate_uc_from_hires_peptide <- function(fit_dat, ## uc filtered dat
                                             fit_values_all, ## fit unfiltered
@@ -62,16 +65,18 @@ create_uc_from_hires_dataset <- function(kin_dat,
 
   return(res)
 }
+
 dat <- omit_amino(alpha_dat, 1)
-kin_dat <- prepare_kin_dat(alpha_dat, state = "Alpha_KSCN")
 kin_dat <- prepare_kin_dat(dat, state = "Alpha_KSCN")
-
+kin_dat <- prepare_kin_dat(alpha_dat, state = "Alpha_KSCN")
 
 fit_k_params <- get_example_fit_k_params()
+
 fit_k_params_2 <- data.frame(
   start = c(k_1 = 2, k_2 = 0.2, k_3 = 0.02),
   lower = c(k_1 = 1, k_2 = 0.1, k_3 = 0.0001),
   upper = c(k_1 = 30, k_2 = 1, k_3 = 0.1))
+
 control <- get_example_control()
 fit_values_all <- create_fit_dataset(kin_dat, control = control,
                                      fit_k_params = fit_k_params_2,
@@ -80,11 +85,11 @@ fit_values_all <- create_fit_dataset(kin_dat, control = control,
 hr_dat <- rbind(create_uc_from_hires_dataset(kin_dat,
                                              fit_values_all,
                                              hires_method = "weighted") %>%
-                  mutate(type = "weighted"),
+                  mutate(type = "weighted average"),
                 hr_dat <- create_uc_from_hires_dataset(kin_dat,
                                                        fit_values_all,
                                                        hires_method = "shortest") %>%
-                  mutate(type = "shortest"))
+                  mutate(type = "shortest peptide"))
 
 mean_err_dat <- mutate(hr_dat, hr_diff2 = hr_diff^2) %>%
   group_by(ID, Sequence, Start, End, State, type) %>%
@@ -94,9 +99,8 @@ mean_err_dat %>%
   ungroup() %>%
   group_by(type) %>%
   mutate(less_05 = mean_err < 0.05) %>%
-  summarise(err = 1 - mean(less_05),
-            no_err = 1 - err,
-            cnt = 106-sum(less_05))
+  summarise(1 - mean(less_05),
+            avg = mean(mean_err))
 
 mean_err_dat %>%
   ungroup() %>%
@@ -167,7 +171,7 @@ p1 <- mean_err_dat %>%
 
 
 
-png("benchmark.png", width = 680, height = 680*1.1)
+png("benchmark.png", width = 680, height = 680*0.9)
 p1/p2 +
   plot_annotation(tag_levels = "A") &
   theme(plot.tag = element_text(size = 24))