diff --git a/R/clusterExpUnitsWithScamp.R b/R/clusterExpUnitsWithScamp.R
index 689fbbe..a597046 100755
--- a/R/clusterExpUnitsWithScamp.R
+++ b/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",
diff --git a/R/discoverPhenotypes.R b/R/discoverPhenotypes.R
index 7ac47ac..b50d8af 100644
--- a/R/discoverPhenotypes.R
+++ b/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
)
diff --git a/R/faust.R b/R/faust.R
index ab16b25..4a1ce08 100755
--- a/R/faust.R
+++ b/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,
diff --git a/R/plotPhenotypeFilter.R b/R/plotPhenotypeFilter.R
index 57f0558..cf3da52 100644
--- a/R/plotPhenotypeFilter.R
+++ b/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",
diff --git a/man/discoverPhenotypes.Rd b/man/discoverPhenotypes.Rd
index e42710e..e839c17 100644
--- a/man/discoverPhenotypes.Rd
+++ b/man/discoverPhenotypes.Rd
@@ -7,7 +7,7 @@
discoverPhenotypes(
gatingSet,
projectPath = normalizePath("."),
- nameOccuranceNum = ceiling((0.5 * length(gatingSet))),
+ nameOccurrenceNumber = ceiling((0.5 * length(gatingSet))),
debugFlag = FALSE,
threadNum = 1,
seedValue = 123,
@@ -32,7 +32,7 @@ final output of \code{faust}, an annotated matrix of counts, is produced at
\code{projectPath/faustData/faustCountMatrix.rds}, and can be loaded into R using
the \code{readRDS} function.}
-\item{nameOccuranceNum}{The number of times a name has to appear in distinct
+\item{nameOccurrenceNumber}{The number of times a name has to appear in distinct
SCAMP clusterings to be gated out.}
\item{debugFlag}{Boolean value. Set to TRUE to print method status information
diff --git a/man/faust.Rd b/man/faust.Rd
index 7ad5180..682e87b 100644
--- a/man/faust.Rd
+++ b/man/faust.Rd
@@ -15,7 +15,7 @@ faust(
projectPath = normalizePath("."),
depthScoreThreshold = 0.01,
selectionQuantile = 0.5,
- nameOccuranceNum = ceiling((0.5 * length(gatingSet))),
+ nameOccurrenceNumber = ceiling((0.5 * length(gatingSet))),
supervisedList = NA,
debugFlag = FALSE,
threadNum = 1,
@@ -116,7 +116,7 @@ empirical quantile is then compared to the depthScoreThreshold for each
marker. All markers with empirical quantile above the depthScoreThreshold
are used by \code{faust} to discover and annotate cell subsets in the experiment.}
-\item{nameOccuranceNum}{The number of times a name has to appear in distinct
+\item{nameOccurrenceNumber}{The number of times a name has to appear in distinct
SCAMP clusterings to be gated out.}
\item{supervisedList}{A list of lists. The names of list entries correspond
diff --git a/reproducibility/simulationStudy/01_runSimulation.R b/reproducibility/simulationStudy/01_runSimulation.R
index 7a51d14..de4e396 100644
--- a/reproducibility/simulationStudy/01_runSimulation.R
+++ b/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,
diff --git a/vignettes/faustIntro.Rmd b/vignettes/faustIntro.Rmd
index 179efdb..51919e9 100644
--- a/vignettes/faustIntro.Rmd
+++ b/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 **faust** in one of two ways.
Each cell in each experimental unit is associated with a full annotation by **faust**.
The number of times a phenotype occurs across the experimental units is counted by **faust**.
-If the resulting number falls below the setting of the `nameOccuranceNum` parameter in the **faust** function,
+If the resulting number falls below the setting of the `nameOccurrenceNumber` parameter in the **faust** function,
all cells associated with that phenotype are labeled "0_0_0_0_0". This is how **faust**
implements phenotypic filtering as described by the manuscript.