@@ -1,7 +1,7 @@

 #' Protein Charge Calculation, Globally

 #'

 #' This function will determine the charge of a peptide using the

-#'   Henderson-Hasselbalch Equation. The output is a data frame (default) or q

+#'   Henderson-Hasselbalch Equation. The output is a data frame (default) or a

 #'   plot of charge calculations along the peptide sequence. Charges are

 #'   determined globally, or along the entire chain.

 #'

@@ -207,7 +207,8 @@ chargeCalculationGlobal <- function(

             hline = 0, dynamicColor = chargeDF$Charge,

             customColors = c("#348AA7", "#92140C", "grey65"),

             customTitle = NA, propertyLimits = c(-1, 1))

-        gg <- gg + ggplot2::labs(title = plotTitle, subtitle = plotSubtitle)

+        gg <- gg + ggplot2::labs(title = plotTitle, subtitle = plotSubtitle,

+                                 y = "Charge")

         return(gg)

     } else {

         return(chargeDF)

@@ -363,7 +364,8 @@ chargeCalculationLocal <- function(sequence, window = 7,  proteinName = NA,

                             hline = 0, dynamicColor = chargeDF$windowCharge,

                             customColors = c("#348AA7", "#92140C", "grey65"),

                             customTitle = NA, propertyLimits = c(-1, 1))

-        gg <- gg + ggplot2::labs(title = plotTitle, subtitle = plotSubtitle)

+        gg <- gg + ggplot2::labs(title = plotTitle, subtitle = plotSubtitle,

+                                 y = "Average Charge")

         return(gg)

     } else {

         return(chargeDF)

@@ -118,7 +118,8 @@ scaledHydropathyLocal <- function(sequence, window = 9,

                         dynamicColor = windowDF$WindowHydropathy,

                         customColors = c("chocolate1", "skyblue3", "grey65"),

                         customTitle = NA, propertyLimits = c(0, 1))

-        gg <- gg + ggplot2::labs(title = plotTitle, subtitle = plotSubtitle)

+        gg <- gg + ggplot2::labs(title = plotTitle, subtitle = plotSubtitle,

+                                 y = "Hydropathy")

         return(gg)

     } else { #returns the DF

         return(windowDF)

@@ -224,7 +225,8 @@ scaledHydropathyGlobal <- function(

                         customColors = c("chocolate1", "skyblue3", "grey65"),

                         customTitle = NA,

                         propertyLimits = c(0, 1))

-        gg <- gg + ggplot2::labs(title = plotTitle, subtitle = plotSubtitle)

+        gg <- gg + ggplot2::labs(title = plotTitle, subtitle = plotSubtitle,

+                                 y = "Hydropathy")

         return(gg)

     } else {

         return(hydropathyDF)

@@ -95,7 +95,8 @@ sequenceCheck <- function(

     }

     #-----

     #This section will confirm what to do with the amino acid sequence

-    if(is(sequence)[1] == "AAString"){

+    if(is(sequence)[1] %in% c("AAString", "BString", 

+                              "AAStringSet", "BStringSet")){

         sequence <- as.character(sequence)

     }

     if (length(sequence) == 1) {

@@ -342,9 +342,13 @@ sequenceMap <- function(

         if (plyr::is.discrete(seqDF$Property)) {

             gg <- gg + ggplot2::scale_fill_manual(values = customColors)

         } else {

-            gg <- gg + ggplot2::scale_fill_gradient2(high = customColors[1],

-                                                        low = customColors[2],

-                                                        mid = customColors[3])

+            gg <- gg + 

+                ggplot2::scale_fill_gradient2(

+                    high = customColors[1],

+                    low = customColors[2],

+                    mid = customColors[3],

+                    midpoint = ((min(seqDF$Property) + max(seqDF$Property)) / 2)

+                )

         }

     }

     return(gg)