Merge pull request #305 from noranekonobokkusu/master

Several fixes
BorchLab · Jan 12, 2024 · db49913 · db49913
2 parents 654be88 + 08e7292
commit db49913
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Showing 3 changed files with 4 additions and 2 deletions.
diff --git a/R/clonalAbundance.R b/R/clonalAbundance.R
@@ -86,6 +86,7 @@ clonalAbundance <- function(input.data,
       Con.df<- rbind.data.frame(Con.df, data1) 
     }
     Con.df <- data.frame(Con.df)
+    Con.df$values <- factor(Con.df$values, levels=names(input.data))
     col <- length(unique(Con.df$values))
     fill <- "Samples"
     if (scale == TRUE) { 

diff --git a/R/clonalQuant.R b/R/clonalQuant.R
@@ -94,10 +94,11 @@ clonalQuant <- function(input.data,
   if(!is.null(group.by)) {
     col <- length(unique(mat[,group.by]))
   }
+  mat[,x] = factor(mat[,x], levels = names(input.data))
 
   #Plotting
   plot <- ggplot(data = mat, 
-                 aes(x=mat[,x], y=mat[,y], fill=as.factor(mat[,x]))) +
+                 aes(x=mat[,x], y=mat[,y], fill=mat[,x])) +
             stat_summary(geom = "errorbar", 
                          fun.data = mean_se, 
                          position = "dodge", 

diff --git a/R/clonalRarefaction.R b/R/clonalRarefaction.R
@@ -68,7 +68,7 @@ clonalRarefaction <- function(input.data,
   mat <- iNEXT(mat.list, q=hill.numbers, datatype="abundance",nboot = n.boots) 
   plot <- suppressMessages(ggiNEXT(mat, type=plot.type) + 
             scale_shape_manual(values = rep(16,col)) + 
-            scale_fill_manual(values = rep("white", col)) + 
+            scale_fill_manual(values = c(.colorizer(palette,col))) + 
             scale_color_manual(values = c(.colorizer(palette,col)))  + 
             theme_classic())
   if (exportTable == TRUE) {