rm unused files; change R.Condition and R.Replicate to string

NAMESPACE

@@ -17,7 +17,6 @@ export(impute.nuc_norm)
 export(impute.pca_bayes)
 export(impute.pca_prob)
 export(normalize)
-export(preProcessFiltering)
 export(preprocessing)
 export(preprocessing_scaffold)
 export(pullProteinPath)

R/filterings.R

@@ -49,7 +49,7 @@
 #' 
 #' @autoglobal
 #' 
-#' @export
+#' @noRd
 
 preProcessFiltering <- function(dataSet,
                                 filterNaN = TRUE,

R/preprocessing.R

@@ -115,6 +115,8 @@ preprocessing <- function(fileName,
 
   ## select columns necessary for analysis
   selectedData <- filteredData %>%
+    mutate(R.Condition = as.character(R.Condition),
+           R.Replicate = as.character(R.Replicate)) %>%
     select(R.Condition, R.Replicate, PG.Quantity, PG.ProteinNames, PG.ProteinAccessions)
 
   ## print summary statistics for full raw data set

R/visualizations.R

@@ -220,8 +220,7 @@ visualize <- function(
   } else if (graphType == "normalize") {
 
     plotData <- dataSet %>%
-      pivot_longer(-c(R.Condition, R.Replicate)) %>%
-      mutate(across(c(R.Condition, R.Replicate), as.character))
+      pivot_longer(-c(R.Condition, R.Replicate))
 
     ggplot(plotData, aes(x = R.Condition, y = value,
                          fill = if (length(unique(R.Replicate)) == 1) R.Condition else R.Replicate)) +

README.md

@@ -47,5 +47,5 @@ build this package.
 2. `sh: /opt/gfortran/bin/gfortran: No such file or directory`
 
 The [GFortran](https://fortran-lang.org/learn/os_setup/install_gfortran/) compiler is
-required to build this package. 
+required to build this package.