Wrapped up pH generalization for DB

ApfeldLab · Jun 14, 2020 · 8966f26 · 8966f26
1 parent e7f54de
commit 8966f26
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Showing 7 changed files with 19 additions and 10 deletions.
diff --git a/R/utils.R b/R/utils.R
@@ -68,7 +68,9 @@ formatSpectraData <-
            values_max,
            lambda_min,
            values_min,
-           sensor_midpoint) {
+           sensor_midpoint,
+           lambda1_recommended,
+           lambda2_recommended) {
     # Data validation -------
 
     # Validating lengths
@@ -148,7 +150,9 @@ formatSpectraData <-
         values_max = values_max,
         lambda_min = lambda_min,
         values_min = values_min,
-        sensor_midpoint = sensor_midpoint
+        sensor_midpoint = sensor_midpoint,
+        lambda1_recommended = lambda1_recommended,
+        lambda2_recommended = lambda2_recommended
       )
     )
   }

diff --git a/docs/articles/accessing-database.html b/docs/articles/accessing-database.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 1.5.1
 pkgdown_sha: ~
 articles:
   accessing-database: accessing-database.html
-last_built: 2020-06-14T14:49Z
+last_built: 2020-06-14T15:17Z
 
diff --git a/docs/reference/formatSpectraData.html b/docs/reference/formatSpectraData.html
diff --git a/inst/shinyApp/server/server_01_welcome.R b/inst/shinyApp/server/server_01_welcome.R
@@ -85,7 +85,6 @@ observeEvent(input$`use-upload`, {
 })
 
 update_sensor_lambda <- observeEvent(input$sensors, {
-  browser()
   if (input$sensors %in% sensorNames) {
     index <- match(input$sensors, sensorData$sensor_name)
     updateNumericInput(session, inputId = "lambda1",

diff --git a/man/formatSpectraData.Rd b/man/formatSpectraData.Rd
diff --git a/vignettes/accessing-database.Rmd b/vignettes/accessing-database.Rmd
@@ -51,14 +51,15 @@ In the following methods, "values_min"/other references to 'min' refer to the li
 lambda_max <- deGFP1$V1
 values_max <- deGFP1$V2
 lambda_min <- deGFP1$V3
-values_max <- deGFP1$V4
+values_min <- deGFP1$V4
 ```
 
 Now, you can use the `sensorOverlord::formatSpectraData` function to format the data into
 a list for submission to the database:
 
 ```R
-submission <- formatSpectraData(name = "deGFP1", type = "pH", readout = "emission ratiometric", lambda_max = lambda_max, values_max = values_max, lambda_min = lambda_min, values_min = values_min, sensor_midpoint = 8.02)
+submission <- formatSpectraData(name = "deGFP1", type = "pH", readout = "emission ratiometric", lambda_max = lambda_max, values_max = values_max, lambda_min = lambda_min, values_min = values_min, sensor_midpoint = 8.02,
+lambda1_recommended = 515, lambda2_recommended = 460)
 ```
 
 Then, when you're ready to submit your entry, you can use `sensorOverlord::getDb()` and `$insert` to add your new submission: