rethinking the log transform

microbiomeDB · Nov 30, 2023 · 603af1d · 603af1d
1 parent 31e1fb6
commit 603af1d
Showing 1 changed file with 15 additions and 13 deletions.
diff --git a/R/ui.R b/R/ui.R
@@ -20,20 +20,22 @@ ui <- shiny::fluidPage(
              shiny::fileInput("fileUpload", shiny::strong("Upload Data Table"), accept = c(".tab", "tsv",".rds")),
              shiny::fileInput("fileUpload2", shiny::strong("Upload Second Data Table (optional)"), accept = c(".tab", "tsv",".rds")),
              shiny::hr(),
-             div(style="display:inline-block",
-              selectInput("correlationMethod", shiny::strong("Correlation Parameters:"),
+             #div(style="display:inline-block",
+              selectInput("correlationMethod", shiny::strong("Correlation Method:"),
                 c("Spearman" = "spearman",
-                  "Pearson" = "pearson"))
-             ),
-             div(style="display:inline-block",
-              shinyWidgets::switchInput("dataAreCompositonal", "log transform", 
-                value = FALSE,
-                onLabel = "Yes",
-                offLabel = "No",
-                size = "normal",
-                inline = TRUE,
-                labelWidth = "100px")
-             ),
+                  "Pearson" = "pearson")),
+             #),
+             # commenting this for now. after reading https://www.nature.com/articles/ismej2015235
+             # i think i want to add more methods and maybe the ability to filter rare taxa prior to correlation
+             #div(style="display:inline-block",
+             # shinyWidgets::switchInput("dataAreCompositonal", "log transform", 
+             #   value = FALSE,
+             #   onLabel = "Yes",
+             #   offLabel = "No",
+             #   size = "normal",
+             #   inline = TRUE,
+             #   labelWidth = "100px")
+             #),
              shiny::p(),
              shiny::numericInput("correlationFilter", shiny::strong("Correlation Coefficient Threshold:"), 0, min = -1, max = 1),
              shiny::plotOutput("correlationHistogram", height = "200px"),