Adds log-scaled intensities. Disables DEV mode

.gitignore

@@ -132,3 +132,5 @@ dmypy.json
 test_app.py
 
 test_confusion_matrix.png
+
+small_example-kopi.csv

design.py

@@ -281,7 +281,14 @@ def design_section(
                     key="intensity_by",
                     label="Intensity based on",
                     default="Counts",
-                    options=["Counts", "Normalized (%)"],
+                    options=[
+                        "Counts",
+                        "Normalized (%)",
+                        "Log Counts",
+                        "Log2 Counts",
+                        "Log10 Counts",
+                        "Arcsinh Counts",
+                    ],
                     get_setting_fn=get_uploaded_setting,
                     type_=str,
                 )

plot.R

@@ -5,7 +5,7 @@ library(dplyr)
 library(ggplot2)
 library(jsonlite)
 
-dev_mode <- TRUE
+dev_mode <- FALSE
 
 option_list <- list(
     make_option(c("--data_path"),
@@ -285,11 +285,8 @@ if (isTRUE(design_settings$show_tile_border)) {
     tile_border_color <- design_settings$tile_border_color
 }
 
-intensity_by <- ifelse(
-    tolower(design_settings$intensity_by) == "counts",
-    "counts",
-    "normalized"
-)
+intensity_by <- tolower(design_settings$intensity_by)
+if (grepl("normalized", intensity_by)) intensity_by <- "normalized"
 
 confusion_matrix_plot <- tryCatch(
     {