@@ -1,6 +1,6 @@

 Package: celda

 Title: CEllular Latent Dirichlet Allocation

-Version: 1.5.11

+Version: 1.5.12

 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",

     role = c("aut", "cre")),

     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),

@@ -168,17 +168,17 @@ setMethod("celdatosce",

         SingleCellExperiment::altExp(sce, altExpName) <- sce

         xClass <- "matrix"

         model <- celdaModel@celdaGridSearchParameters$model

-        paramsTest <- celdaCGGridSearchRes@celdaGridSearchParameters$paramsTest

+        paramsTest <- celdaModel@celdaGridSearchParameters$paramsTest

         paramsFixed <-

-            celdaCGGridSearchRes@celdaGridSearchParameters$paramsFixed

-        maxIter <- celdaCGGridSearchRes@celdaGridSearchParameters$maxIter

-        nchains <- celdaCGGridSearchRes@celdaGridSearchParameters$nchains

-        cores <- celdaCGGridSearchRes@celdaGridSearchParameters$cores

-        bestOnly <- celdaCGGridSearchRes@celdaGridSearchParameters$bestOnly

-        perplexity <- celdaCGGridSearchRes@celdaGridSearchParameters$perplexity

-        verbose <- celdaCGGridSearchRes@celdaGridSearchParameters$verbose

+            celdaModel@celdaGridSearchParameters$paramsFixed

+        maxIter <- celdaModel@celdaGridSearchParameters$maxIter

+        nchains <- celdaModel@celdaGridSearchParameters$nchains

+        cores <- celdaModel@celdaGridSearchParameters$cores

+        bestOnly <- celdaModel@celdaGridSearchParameters$bestOnly

+        perplexity <- celdaModel@celdaGridSearchParameters$perplexity

+        verbose <- celdaModel@celdaGridSearchParameters$verbose

         logfilePrefix <-

-            celdaCGGridSearchRes@celdaGridSearchParameters$logfilePrefix

+            celdaModel@celdaGridSearchParameters$logfilePrefix

         altExp <- .createSCEceldaGridSearch(celdaList = celdaModel,

             sce = SingleCellExperiment::altExp(sce, altExpName),

@@ -807,6 +807,9 @@ setMethod("plotGridSearchPerplexityDiff",

 .plotGridSearchPerplexityDiffCG <- function(celdaList, sep, n) {

+    # fix check note

+    K <- L <- perpdiffK <- meanperpdiffK <- perpdiffL <- meanperpdiffL <- NULL

+

     if (!all(c("K", "L") %in% colnames(runParams(celdaList)))) {

         stop("runParams(celdaList) needs K and L columns.")

     }

@@ -905,6 +908,7 @@ setMethod("plotGridSearchPerplexityDiff",

 .plotGridSearchPerplexityDiffC <- function(celdaList, sep, n) {

+    K <- perpdiffK <- meanperpdiffK <- NULL # fix check note

     if (!all(c("K") %in% colnames(runParams(celdaList)))) {

         stop("runParams(celdaList) needs the column K.")

     }

@@ -959,6 +963,7 @@ setMethod("plotGridSearchPerplexityDiff",

 .plotGridSearchPerplexityDiffG <- function(celdaList, sep, n) {

+    L <- perpdiffL <- meanperpdiffL <- NULL # fix check note

     if (!all(c("L") %in% colnames(runParams(celdaList)))) {

         stop("runParams(celdaList) needs the column L.")

     }

@@ -160,6 +160,8 @@ plotDecontXMarkerPercentage <- function(x, markers, groupClusters = NULL,

                                         exactMatch = TRUE, by = "rownames",

                                         ncol = round(sqrt(length(markers))),

                                         labelBars = TRUE, labelSize = 3) {

+  cellTypeLabels <- percent <- NULL # fix check note

+

   legend <- "none"

   # Check that list arguments are named

   if (!is(markers, "list") || is.null(names(markers))) {

@@ -224,9 +226,9 @@ plotDecontXMarkerPercentage <- function(x, markers, groupClusters = NULL,

   df <- cbind(df, markerLabels = names(markers)[df$markers])

   df$markerLabels <- factor(df$markerLabels, levels = names(markers))

-  plt <- ggplot2::ggplot(df, ggplot2::aes(

-    x = cellTypeLabels,

-    y = percent, fill = assay

+  plt <- ggplot2::ggplot(df, ggplot2::aes_string(

+    x = "cellTypeLabels",

+    y = "percent", fill = "assay"

   )) +

     ggplot2::geom_bar(

       stat = "identity",

@@ -1008,7 +1008,7 @@ setMethod("plotDimReduceCluster",

     ) +

       ggrepel::geom_text_repel(

         data = centroid,

-        mapping = ggplot2::aes(label = Cluster),

+        mapping = ggplot2::aes_string(label = "Cluster"),

         size = labelSize

       )

   }