Merge pull request #40 from hancockinformatics/fix_size_scale_plot

Updated dot size scaling plot

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ABCindex
 Title: A Shiny app to calculate ABCI for checkerboard assays
-Version: 0.99.73
+Version: 0.99.75
 Authors@R:
   person(given = "Travis",
          family = "Blimkie",

_colours.R → _helpers.R

@@ -1,4 +1,7 @@
+# Load packages -----------------------------------------------------------
+
 library(dplyr)
+library(ggplot2)
 
 
 # Standard palettes -------------------------------------------------------
@@ -52,3 +55,41 @@ preset_palettes_split <- list(
 )
 
 saveRDS(preset_palettes_split, "data/preset_palettes_split.Rds")
+
+
+# Dot size scaling plot ---------------------------------------------------
+
+N1S2 <- readRDS("data/size_mapping_N1S2.Rds") %>%
+  mutate(`Linear Scale` = seq(0, 100)) %>%
+  rename("ABCindex" = N1S2) %>%
+  tidyr::pivot_longer(-reference, names_to = "type", values_to = "dot_size") %>%
+  mutate(type = factor(type, c("Linear Scale", "ABCindex")))
+
+ggplot(N1S2, aes(reference, dot_size, group = type, colour = type)) +
+  geom_line(linewidth = 2) +
+  scale_colour_manual(values = c("ABCindex" = "#00c000", "Linear Scale" = "#a00000")) +
+  labs(
+    x = "% Biomass reduction",
+    y = "Dot size",
+    colour = NULL,
+    title = "Dot plot scaling",
+    subtitle = "ABCindex"
+  ) +
+  scale_x_continuous(
+    breaks = seq(0, 100, 20),
+    expand = expansion(mult = c(0, 0.02))
+  ) +
+  scale_y_continuous(
+    breaks = seq(0, 100, 20),
+    expand = expansion(mult = c(0, 0.02))
+  ) +
+  theme(
+    title = element_text(face = "bold"),
+    plot.subtitle = element_text(face = "plain"),
+    legend.text.align = 0,
+    legend.position = c(0.79, 0.2),
+    legend.background = element_blank(),
+    legend.key.width = unit(12, "mm"),
+    legend.key.height = unit(9, "mm")
+  )
+ggsave(width = 7, height = (7 * 0.85), "www/help/dot_size_scaling.png", dpi = 300)

www/help/help.html

@@ -501,7 +501,7 @@ <h2 class="accordion-header">
             </p>
             <p>
               Below, you can see the exact relationship between the percentage
-              of biofilm killed and the default dot size used by ABCindex.
+              of biomass killed and the default dot size used by ABCindex.
             </p>
             <img src="help/dot_size_scaling.png" alt="Dot size scaling" class="center img-fluid" style="width:50%">
           </div>