missing tiles fixed #106

hadexversum · May 19, 2022 · e8bd0aa · e8bd0aa
1 parent 9afa1d2
commit e8bd0aa
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Showing 2 changed files with 6 additions and 6 deletions.
diff --git a/R/calculate_p_value.R b/R/calculate_p_value.R
@@ -74,9 +74,9 @@ calculate_p_value <- function(dat,
     st_2 <- vol_dat[i, "masses_2"][[1]]
 
     if(length(st_1) == 1 | all(st_1 == st_2)) {
-      p_value <- -1
+      p_value <- NA
     } else if (length(st_2) == 1){
-      p_value <- -1
+      p_value <- NA
     } else {
       p_value <- t.test(x = st_1, y = st_2, paired = FALSE, alternative = "two.sided", conf.level = confidence_level)$p.value
     }
@@ -88,8 +88,7 @@ calculate_p_value <- function(dat,
                End = vol_dat[i, "End"],
                P_value = p_value)
 
-  }) %>% bind_rows() %>%
-    filter(P_value > 0)
+  }) %>% bind_rows() 
 
   p_dat[["P_value"]] <- p.adjust(p_dat[["P_value"]], method = p_adjustment_method)
 

diff --git a/R/plot_differential_chiclet.R b/R/plot_differential_chiclet.R
@@ -136,7 +136,7 @@ plot_differential_chiclet <- function(diff_uptake_dat = NULL,
     x_threshold <- t_value * mean(plot_dat[["err_value"]], na.rm = TRUE)/sqrt(length(plot_dat))
 
     chiclet_differential_plot <- chiclet_differential_plot +
-      geom_tile(data = subset(plot_dat, abs(value) < x_threshold), fill = "azure3")
+      geom_tile(data = subset(plot_dat, abs(value) < x_threshold), fill = "grey91")
 
   }
 
@@ -148,7 +148,8 @@ plot_differential_chiclet <- function(diff_uptake_dat = NULL,
       merge(plot_dat, by = c("Sequence", "Start", "End", "Exposure", "ID"))
 
     chiclet_differential_plot <- chiclet_differential_plot +
-      geom_tile(data = subset(diff_uptake_dat, !valid), aes(x = ID, y = Exposure), fill = "grey77")
+      geom_tile(data = subset(diff_uptake_dat, !valid), aes(x = ID, y = Exposure), fill = "grey89") +
+      geom_tile(data = subset(diff_uptake_dat, is.na(valid)), aes(x = ID, y = Exposure), fill = "grey56")
 
   }