Merge branch 'main' of https://github.com/DavidRach/Luciernaga

Author: DavidRach

DESCRIPTION

@@ -19,7 +19,7 @@ Encoding: UTF-8
 LazyData: FALSE
 URL: https://davidrach.github.io/Luciernaga/
 BugReports: https://github.com/DavidRach/Luciernaga/issues
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Imports: 
     Biobase,
     BiocGenerics,

NAMESPACE

@@ -28,8 +28,10 @@ export(Luciernaga_Unmix)
 export(MarginClean)
 export(NameCleanUp)
 export(QC_Amalgamate)
+export(QC_ChorusPDF)
 export(QC_FilePrep_DailyQC)
 export(QC_FilePrep_LJTracking)
+export(QC_FlowSightPDF)
 export(QC_GainMonitoring)
 export(QC_LibraryParse)
 export(QC_Plots)
@@ -209,6 +211,7 @@ importFrom(lubridate,hour)
 importFrom(lubridate,mdy)
 importFrom(lubridate,mdy_hm)
 importFrom(lubridate,mdy_hms)
+importFrom(lubridate,parse_date_time)
 importFrom(lubridate,wday)
 importFrom(lubridate,weeks)
 importFrom(lubridate,ymd)
@@ -218,6 +221,7 @@ importFrom(openCyto,gatingTemplate)
 importFrom(openCyto,gt_gating)
 importFrom(patchwork,plot_spacer)
 importFrom(patchwork,wrap_plots)
+importFrom(pdftools,pdf_text)
 importFrom(plotly,ggplotly)
 importFrom(progressr,progressor)
 importFrom(progressr,with_progress)

R/MagesCauldron.R

@@ -12,6 +12,7 @@
 #' @param device Desired storage format, default is "png"
 #' @param width Desired height for saved plot, default is 15
 #' @param height Desired height for saved plot, default  is 15
+#' @param NumberDetectors Default NULL, used when unstained is NULL
 #' 
 #' @importFrom dplyr mutate
 #' @importFrom dplyr relocate
@@ -43,27 +44,39 @@
 #' @noRd
 MagesCauldron <- function(panelfluors, unstained, returnType="plot", savePlot=FALSE,
    outpath=NULL, filename=NULL, device="png", width=15, height=15, swapname=NULL,
-   swapvalue=NULL){
+   swapvalue=NULL, NumberDetectors=NULL){
 
+  if (!is.null(unstained)){
   DetectorLength <- ncol(unstained)
 
   if (any(unstained > 1)){
     unstained[unstained < 0] <- 0
     A <- do.call(pmax, unstained)
     unstained <- unstained/A
   }
+  
+  TheUnstained <- unstained |> mutate(Fluorophore="Unstained") |>
+    relocate(Fluorophore, .before=1)
+  } else {
+    if (is.null(NumberDetectors)){
+      stop("When not providing unstained, provide NumberDetectors argument")
+    }
+    DetectorLength <- NumberDetectors
+    }
 
   Vaiya <- InstrumentReferences(NumberDetectors = DetectorLength)
-  TheUnstained <- unstained |> mutate(Fluorophore="Unstained") |>
-       relocate(Fluorophore, .before=1)
   TheseFluorophores <- panelfluors
   Data <- Vaiya |> filter(Fluorophore %in% TheseFluorophores)
   Data <- Data |> select(-Instrument)
   Data <- Data |> pivot_wider(names_from="Detector",
    values_from="AdjustedY")
+  
+  if (!is.null(unstained)){
   colnames(TheUnstained) <- gsub("-A", "", gsub("-H", "", colnames(TheUnstained)))
   Data <- bind_rows(Data, TheUnstained)
   TheseFluorophores <- c(TheseFluorophores, paste0("Unstained", seq_len(nrow(unstained))))
+  }
+
   Data$Fluorophore <- factor(Data$Fluorophore, levels=TheseFluorophores)
   Data <- Data |> arrange(desc(Fluorophore))
   Data <- Data |> arrange(Fluorophore)