@@ -143,9 +143,9 @@ generatePrototypes <- function(data, verbose = FALSE, size = NULL) {

       size <- size

     }

-    message(paste("Optimal Grid Size is: ", size))

+    message("Optimal Grid Size is: ", size)

   } else {

-    message(paste("You have provided a grid size of:", size * size))

+    message("You have provided a grid size of:", size * size)

   }

   # genearte the som grid based on the computed grid size

@@ -255,7 +255,7 @@ runFuseSOM <- function(data, markers = NULL, numClusters = NULL, assay = NULL,

   # if we have a dataframe or a matrix

   if (is(data, "data.frame") || is(data, "matrix")) {

-    message(paste("You have provided a dataset of class", class(data)[[1]]))

+    message("You have provided a dataset of class ", class(data)[[1]])

     # if no markers are given, make sure all the columns are numeric

     if (is.null(markers)) {

       numNumeric <- sum(apply(data, 2, function(x) is.numeric(x)))

@@ -269,11 +269,11 @@ runFuseSOM <- function(data, markers = NULL, numClusters = NULL, assay = NULL,

     }

   } else if (is(data, "SingleCellExperiment") || is(data, "SpatialExperiment")) { # if we have a single cell experiment object

     flag <- TRUE

-    message(paste("You have provided a dataset of class", class(data)[[1]]))

+    message("You have provided a dataset of class ", class(data)[[1]])

     # make sure an assay is provided

     if (is.null(assay)) {

-      stop(paste("If a", class(data)[[1]], "make sure the appropriate assay is provided as well"))

+      stop("If a ", class(data)[[1]], " make sure the appropriate assay is provided as well")

     }

     dataNew <- t(assay(data, assay))

@@ -389,7 +389,7 @@ estimateNumCluster <- function(data,

   # if we have a single cell experiment or spatial experiment object

   if (is(data, "SingleCellExperiment") || is(data, "SpatialExperiment")) {

     flag <- TRUE

-    message(paste("You have provided a dataset of class:", class(data)[[1]]))

+    message("You have provided a dataset of class: ", class(data)[[1]])

     somModel <- data@metadata$SOM

   } else { # if we just have the som model

     somModel <- data

@@ -482,7 +482,7 @@ optiPlot <- function(data, method = "jump") {

   # if we have a single cell experiment object

   if (is(data, "SingleCellExperiment") || is(data, "SpatialExperiment")) {

-    message(paste("You have provided a dataset of class:", class(data)[[1]]))

+    message("You have provided a dataset of class: ", class(data)[[1]])

     kEst <- data@metadata$clusterEstimation

   } else { # if we just have the som model

     kEst <- data