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.