From ea922f2d9920a18f762dd42184bf02d10e73228f Mon Sep 17 00:00:00 2001
From: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: Thu, 25 Apr 2024 14:03:33 -0700
Subject: [PATCH] Changes to size scaling method for dot and split dot plots.

---
 DESCRIPTION   |  2 +-
 R/2_upload.R  |  2 +-
 R/3_results.R | 34 ++++++++++++++++++----------------
 3 files changed, 20 insertions(+), 18 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 92c0151..2a14ae7 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ABCindex
 Title: A Shiny app to calculate ABCI for checkerboard assays
-Version: 0.99.80
+Version: 0.99.801
 Authors@R:
   person(given = "Travis",
          family = "Blimkie",
diff --git a/R/2_upload.R b/R/2_upload.R
index a9304ff..892dff9 100644
--- a/R/2_upload.R
+++ b/R/2_upload.R
@@ -133,7 +133,7 @@ abci_analysis_single <- function(
     )
 
   if (!normalize) {
-    if (max(data_clean[[col.data]]) >= 50) {
+    if (max(data_clean[[col.data]]) - min(data_clean[[col.data]]) > 10) {
       data_clean[[col.data]] <- data_clean[[col.data]] / 100
     }
   }
diff --git a/R/3_results.R b/R/3_results.R
index dbe70ea..54df3a8 100644
--- a/R/3_results.R
+++ b/R/3_results.R
@@ -544,12 +544,14 @@ plot_dot <- function(
 
   # Fix up the variable being mapped to size. Define labels and breaks.
   data <- data %>%
-    group_by(.data[[col.analysis]]) %>%
     mutate(
       across(all_of(c(x.drug, y.drug)), forcats::fct_inseq),
-      reference = ceiling(scales::rescale(.data[[col.size]], to = c(0, 100)))
+      reference = ifelse(
+        test = ceiling(.data[[col.size]] * 100) <= 100,
+        yes = ceiling(.data[[col.size]] * 100),
+        no = 100
+      )
     ) %>%
-    ungroup() %>%
     left_join(size_mapping, by = "reference")
 
   proper_labels <- seq(0, 100, 20)
@@ -830,12 +832,14 @@ plot_dot_split <- function(
 
   # Fix up the variable being mapped to size. Define labels and breaks.
   data <- data %>%
-    group_by(.data[[col.analysis]]) %>%
     mutate(
       across(all_of(c(x.drug, y.drug)), forcats::fct_inseq),
-      reference = ceiling(scales::rescale(.data[[col.size]], to = c(0, 100)))
+      reference = ifelse(
+        test = ceiling(.data[[col.size]] * 100) <= 100,
+        yes = ceiling(.data[[col.size]] * 100),
+        no = 100
+      )
     ) %>%
-    ungroup() %>%
     left_join(size_mapping, by = "reference")
 
   proper_labels <- seq(0, 100, 20)
@@ -849,13 +853,11 @@ plot_dot_split <- function(
   if (!large.effect) {
     data <- mutate(data, large_chr = rep(0))
   } else {
-    data <- data %>%
-      mutate(
-        large_chr = ifelse(
-          (effect_avg > large.effect.val & data[[col.fill]] > abci.val),
-          yes = 1,
-          no = 0)
-      )
+    data <- mutate(data, large_chr = ifelse(
+      test = (effect_avg > large.effect.val & data[[col.fill]] > abci.val),
+      yes = 1,
+      no = 0
+    ))
   }
 
   # MICs are calculated by `get_mic()` and converted to positions on the axes
@@ -976,9 +978,9 @@ plot_dot_split <- function(
       x,
       col_size = scales::rescale(N1S2, to = size.range),
       col_size = ifelse(
-        !is.na(col_fill),
-        col_size,
-        0
+        test = !is.na(col_fill),
+        yes = col_size,
+        no = 0
       )
     )
   })