Some updates to make sure package buils correctly in GitHub actions, bumping to 0.99.3

Author: DavidRach

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: Luciernaga
 Type: Package
 Title: Tools for the evaluation of Spectral Flow Cytometry (SFC) unmixing controls 
-Version: 0.99.2
+Version: 0.99.3
 Authors@R: 
     person("David", "Rach", , "drach@som.umaryland.edu", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-2235-5585"))
@@ -23,6 +23,7 @@ RoxygenNote: 7.3.2
 Imports: 
     Biobase,
     BiocGenerics,
+    data.table,
     dplyr,
     figpatch,
     flowCore,
@@ -56,15 +57,13 @@ Imports:
     uwot,
     xml2,
     zoo
-Depends: R (>= 4.4.0)
+Depends: R (>= 4.5.0)
 Suggests: 
     BiocStyle,
-    data.table,
     CytoML,
     DataEditR,
     DT,
     knitr,
-    openCyto,
     RColorBrewer,
     rmarkdown,
     shiny,

NAMESPACE

@@ -201,6 +201,7 @@ importFrom(stats,loess)
 importFrom(stats,lsfit)
 importFrom(stats,mad)
 importFrom(stats,median)
+importFrom(stats,na.omit)
 importFrom(stats,quantile)
 importFrom(stats,rlnorm)
 importFrom(stats,rnorm)

R/DashboardHelpers.R

@@ -32,7 +32,7 @@ utils::globalVariables(c("%rCV", ".", ".data", "AdjustedY", "AggregateName",
 #' @importFrom tidyselect all_of
 #' @importFrom dplyr slice
 #' @importFrom dplyr pull
-#' 
+#' @importFrom stats na.omit
 #' @return Some value
 #' 
 #' @noRd

R/Luciernaga_BrightnessOverTime.R

@@ -4,6 +4,7 @@
 #' @param columnname The columnname for Cluster, becomes the categorical defining lines and dots
 #' @param datename The column name for Experiment/Dates, becomes the x-axis
 #' @param Detector Default NULL, specify a detector, overrides the y-axis
+#' @param plotType Something
 #' 
 #' @importFrom stringr str_detect
 #' @importFrom dplyr pull

R/Luciernaga_Cosine.R

@@ -2,7 +2,8 @@
 #'
 #' @param data A data.frame with a single name column and rest numeric columns
 #' @param returntype Default returns "plot", alternatively "matrix" for underlying data
-#'
+#' @param rearrange Something
+#' 
 #' @importFrom dplyr select
 #' @importFrom tidyselect where
 #' @importFrom lsa cosine

R/QC_SimilarFluorophores.R

@@ -5,7 +5,8 @@
 #' @param NumberHits Number of most similar fluorophores by cosine
 #' @param returnSynonymns Returns only fluorophores > 0.98 cosine value, default FALSE
 #' @param returnPlots Whether to also return signature plots, default is set FALSE
-#'
+#' @param returnSynonyms Something
+#' 
 #' @importFrom dplyr filter
 #' @importFrom dplyr slice
 #' @importFrom dplyr mutate
@@ -29,8 +30,8 @@
 #' Results <- QC_SimilarFluorophores(TheFluorophore="Spark Blue 550",
 #'  NumberDetectors=64, returnSynonymns=FALSE, NumberHits = 10, returnPlots=FALSE)
 
-QC_SimilarFluorophores <- function(TheFluorophore, NumberDetectors, returnSynonyms=FALSE,
-  NumberHits=10, returnPlots=FALSE) {
+QC_SimilarFluorophores <- function(TheFluorophore, NumberDetectors,
+   returnSynonyms=FALSE, NumberHits=10, returnPlots=FALSE) {
 
   ReferenceData <- Luciernaga:::InstrumentReferences(NumberDetectors=NumberDetectors)
   #nrow(ReferenceData)

R/QC_ViewSignature.R

@@ -1,7 +1,7 @@
 #' Visualizes the Signature for given row in an averaged signature data.frame.
 #'
 #' @param x Name in the Sample column you want to filter for
-#' @param columname Default is Sample, specifies column name from which x is filtered from 
+#' @param columnname Default is Sample, specifies column name from which x is filtered from 
 #' @param data A data.frame object from QC_LibraryParse containing Fluorophore name column 
 #' and numeric detector columns.
 #' @param Normalize Whether to normalize the data based on peak detector value, default is TRUE

R/RCVfromFCS.R

@@ -3,6 +3,8 @@
 #' @param x The Gating Set object being iterated
 #' @param subset The Gating Set subset for population of interest
 #' @param sample.name The keyword corresponding to the samples name
+#' @param experiment.name Something
+#' @param condition.name Something
 #' 
 #' @importFrom flowCore keyword
 #' @importFrom flowWorkspace gs_pop_get_data

R/SimulatedData.R

@@ -62,7 +62,7 @@ NoisyMatrix <- as.matrix(NoisyDataset)
 
 path <- system.file("extdata", package = "Luciernaga")
 files <- list.files(path=path, pattern="CD4_BUV805.*Cells", full.names=TRUE)
-CytoSet <- load_cytoset_from_fcs(files, truncate_max_range = FALSE, transform = FALSE)
+CytoSet <- load_cytoset_from_fcs(files, truncate_max_range = FALSE, transformation = FALSE)
 fr <- CytoSet[[1, returnType = "flowFrame"]]
 Parameter <- fr@parameters
 Parameter@data <- ParameterParam

R/TransformationCheck.R

@@ -10,6 +10,11 @@
 #' @param widthBasis Argument
 #' @param Multiple Argument
 #' @param returnType Argument
+#' @param optionalY Something
+#' @param optionalX Something
+#' @param optionalOutpath Something
+#' @param optionalBins Something
+#' @param optionalName Something
 #' 
 #' @importFrom flowWorkspace load_cytoset_from_fcs
 #' @importFrom flowWorkspace GatingSet