Documentation tweaks.

Better error message if using old Vision object

Signed-off-by: David DeTomaso <davedeto@gmail.com>

Author: deto

R/Server.R

@@ -31,7 +31,7 @@ ServerSigProjMatrix <- function(zscores, pvals, proj_labels, sig_labels) {
 #' @return JSON formatted Signature object.
 signatureToJSON <- function(sig) {
 
-    # Pass in a Signature object from a FastProject Object to be converted into a JSON object
+    # Pass in a Signature object from an R Object to be converted into a JSON object
     sig@sigDict <- as.list(sig@sigDict)
 
     json <- toJSON(sig, force=TRUE, pretty=TRUE, auto_unbox=TRUE)
@@ -100,7 +100,7 @@ coordinatesToJSON <- function(p) {
     return(json)
 }
 
-#' Converts a sigProjMatrix from a FastProject Object to a JSON object
+#' Converts a sigProjMatrix from an R Object to a JSON object
 #' @importFrom jsonlite toJSON
 #' @param sigzscores Matrix of signature z-scores
 #' @param sigpvals Matrix of signature p-values
@@ -156,8 +156,7 @@ compressJSONResponse <- function(json, res, req){
 #' Lanch the server
 #' @importFrom jsonlite fromJSON
 #' @importFrom utils browseURL URLdecode stack
-#' @param object FastProject object or path to a file containing such an
-#' object (saved using saveAndViewResults, or directly using saveRDS)
+#' @param object Vision object
 #' @param port The port on which to serve the output viewer.  If omitted, a
 #' random port between 8000 and 9999 is chosen.
 #' @param host The host used to serve the output viewer. If omitted, "127.0.0.1"

R/SigScoreMethods.R

@@ -1,10 +1,10 @@
 #' Different ways to evalutate the signature score
 #'
-#' EAch method should have the same signature so they can be swapped
+#' Each method should have the same signature so they can be swapped
 #'
 #' Right now, each takes in a wrapped data object and signature object
 #'
-#' Specified by FastProject argument (sig_score_method), default = naiveEvalSignature
+#' Specified by Vision argument (sig_score_method), default = "naive"
 
 #' Evaluate signature scores efficiently in batches
 #'

R/Utilities.R

@@ -35,15 +35,15 @@ batchify <- function(items, per_batch, n_workers = 1) {
 }
 
 
-#' Check's the version of the FastProject object and displays error if necessary
+#' Checks the version of the Vision object and displays error if necessary
 #'
-#' @param object FastProject object
+#' @param object Vision object
 #' @return NULL
 versionCheck <- function(object) {
 
     templateStr <- paste0(
-        "This FastProject object was created with an older version of the library.",
-        "  To view, either install an older version (commit #COMMIT) from GitHub (www.github.com/YosefLab/FastProjectR) or",
+        "This Vision object was created with an older version of the library.",
+        "  To view, either install an older version (commit #COMMIT) from GitHub (www.github.com/YosefLab/Vision) or",
         " recreate the object and re-run analyze"
     )
 
@@ -57,6 +57,11 @@ versionCheck <- function(object) {
         stop(msg, call. = FALSE)
     }
 
+    if(object@version < 1.1) {
+        msg <- gsub("#COMMIT", "2db4552", templateStr)
+        stop(msg, call. = FALSE)
+    }
+
     # Add new commit hashes here as version increases and breaks backward compatibility
 
     return()