Change nameOccurranceNum to nameOccurrenceNumber

R/clusterExpUnitsWithScamp.R

@@ -141,7 +141,7 @@
 
 
 .clusterExpUnitsWithScamp <- function(projectPath,
-                                      nameOccuranceNum,
+                                      nameOccurrenceNumber,
                                       debugFlag,
                                       threadNum,
                                       seedValue,
@@ -349,11 +349,11 @@
                                         length(which(nameSummary >= x))}))
 
     elbowLoc <- .computeElbow(nameSummaryPlotDF)
-    if (nameOccuranceNum > 0) {
+    if (nameOccurrenceNumber > 0) {
         #the user has set this value
-        clusterNames <- names(nameSummary[which(nameSummary >= nameOccuranceNum)])
+        clusterNames <- names(nameSummary[which(nameSummary >= nameOccurrenceNumber)])
         saveRDS(
-            nameOccuranceNum,
+            nameOccurrenceNumber,
             file.path(normalizePath(projectPath),
                       "faustData",
                       "metaData",

R/discoverPhenotypes.R

@@ -16,7 +16,7 @@
 #' `projectPath/faustData/faustCountMatrix.rds`, and can be loaded into R using
 #' the `readRDS` function.
 #'
-#' @param nameOccuranceNum The number of times a name has to appear in distinct
+#' @param nameOccurrenceNumber The number of times a name has to appear in distinct
 #' SCAMP clusterings to be gated out.
 #'
 #' @param debugFlag Boolean value. Set to TRUE to print method status information
@@ -119,7 +119,7 @@
 #' @md
 discoverPhenotypes <- function(gatingSet,
                                projectPath=normalizePath("."),
-                               nameOccuranceNum=0,
+                               nameOccurrenceNumber=0,
                                debugFlag=FALSE,
                                threadNum=1,
                                seedValue=123,
@@ -155,7 +155,7 @@ discoverPhenotypes <- function(gatingSet,
     if (debugFlag) print("Discovering phenotypes across experimental units.")
     .clusterExpUnitsWithScamp(
         projectPath = projectPath,
-        nameOccuranceNum = nameOccuranceNum,
+        nameOccurrenceNumber = nameOccurrenceNumber,
         debugFlag = debugFlag,
         threadNum = threadNum,
         seedValue = seedValue,
@@ -167,7 +167,7 @@ discoverPhenotypes <- function(gatingSet,
 
     .plotPhenotypeFilter(
         projectPath=projectPath,
-        nameOccuranceNum=nameOccuranceNum,
+        nameOccurrenceNumber=nameOccurrenceNumber,
         plottingDevice=plottingDevice
     )
 

R/faust.R

@@ -89,7 +89,7 @@
 #' marker. All markers with empirical quantile above the depthScoreThreshold
 #' are used by `faust` to discover and annotate cell subsets in the experiment.
 #'
-#' @param nameOccuranceNum The number of times a name has to appear in distinct
+#' @param nameOccurrenceNumber The number of times a name has to appear in distinct
 #' SCAMP clusterings to be gated out.
 #'
 #' @param supervisedList A list of lists. The names of list entries correspond
@@ -223,7 +223,7 @@ faust <- function(gatingSet,
                   projectPath=normalizePath("."),
                   depthScoreThreshold=0.01,
                   selectionQuantile=0.50,
-                  nameOccuranceNum=0,
+                  nameOccurrenceNumber=0,
                   supervisedList=NA,
                   debugFlag=FALSE,
                   threadNum=1,
@@ -267,7 +267,7 @@ faust <- function(gatingSet,
         discoverPhenotypes(
             gatingSet = gatingSet,
             projectPath = projectPath,
-            nameOccuranceNum = nameOccuranceNum,
+            nameOccurrenceNumber = nameOccurrenceNumber,
             debugFlag = debugFlag,
             threadNum = threadNum,
             seedValue = seedValue,

R/plotPhenotypeFilter.R

@@ -1,6 +1,6 @@
 .plotPhenotypeFilter <- function(
                                  projectPath,
-                                 nameOccuranceNum,
+                                 nameOccurrenceNumber,
                                  plottingDevice
                                  )
 {
@@ -24,7 +24,7 @@
         geom_vline(xintercept=elbowLoc,col="red")+
         xlab("Number of times a phenotype appears across clusterings")+
         ylab("Number of phenotypes exceeding the appearance number")+
-        ggtitle("Red line is nameOccuranceNum setting in faust")
+        ggtitle("Red line is nameOccurrenceNumber setting in faust")
 
     fpNameOut <- file.path(normalizePath(projectPath),
                            "faustData",

reproducibility/simulationStudy/01_runSimulation.R

@@ -216,7 +216,7 @@ faust:::faust(
     depthScoreThreshold = 0.01,
     selectionQuantile = 0.5,
     drawAnnotationHistograms = FALSE,
-    nameOccuranceNum = max(1,floor(length(gs)/4)),
+    nameOccurrenceNumber = max(1,floor(length(gs)/4)),
     debugFlag = TRUE,
     threadNum = 10,
     seedValue = 12345,

vignettes/faustIntro.Rmd

@@ -250,7 +250,7 @@ faust(
   debugFlag = FALSE,
   #set this to the number of threads you want to use on your system
   threadNum = parallel::detectCores() / 2 - 1,
-  nameOccuranceNum=1,
+  nameOccurrenceNumber=1,
   seedValue = 271828,
   annotationsApproved = FALSE # set to false before we inspect the scores plots.
 ) 
@@ -283,7 +283,7 @@ faust(
   debugFlag = FALSE,
   #set this to the number of threads you want to use on your system
   threadNum = parallel::detectCores() / 2 - 1,
-  nameOccuranceNum=1,
+  nameOccurrenceNumber=1,
   seedValue = 271828,
   annotationsApproved = TRUE
 )
@@ -331,7 +331,7 @@ The last column is the "not annotated" subset, which **<span style="color:skyblu
 Cells are given the generic label by **<span style="color:skyblue">faust</span>** in one of two ways.
 Each cell in each experimental unit is associated with a full annotation by **<span style="color:skyblue">faust</span>**.
 The number of times a phenotype occurs across the experimental units is counted by **<span style="color:skyblue">faust</span>**.
-If the resulting number falls below the setting of the `nameOccuranceNum` parameter in the **<span style="color:skyblue">faust</span>** function,
+If the resulting number falls below the setting of the `nameOccurrenceNumber` parameter in the **<span style="color:skyblue">faust</span>** function,
 all cells associated with that phenotype are labeled "0_0_0_0_0". This is how **<span style="color:skyblue">faust</span>**
 implements phenotypic filtering as described by the manuscript.