fixed most vdiffr tests except startrac and clonalBias

R/clonalBias.R

@@ -104,9 +104,14 @@ clonalBias <- function(sc.data,
     bias$cloneSize[i] <- as.vector(meta[which(meta[,cloneCall] == clone & meta[,split.by] == split),"cloneSize"])[1]
   }
 
-  bias$cloneSize <- factor(bias$cloneSize , rev(levels(meta[,"cloneSize"])))
-  #Plotting 
-  plot <- ggplot(bias, aes(x=ncells,y=bias)) + 
+  bias$cloneSize <- factor(bias$cloneSize , rev(levels(meta[, "cloneSize"])))
+
+  if (exportTable) {
+    return(bias)
+  }
+
+  #else, return the plot 
+  ggplot(bias, aes(x=ncells,y=bias)) + 
     geom_point(aes(fill=Top_state, size = cloneSize), shape = 21, stroke = 0.25) + 
     stat_quantile(data=df_shuffle, 
                          quantiles = c(corrected_p), 
@@ -115,13 +120,9 @@ clonalBias <- function(sc.data,
                          color = "black", 
                          lty = 2) + 
     scale_fill_manual(values = .colorizer(palette,  length(unique(bias[,"Top_state"])))) + 
-    theme_classic() + 
-    xlab("Clone Size") + 
+    theme_classic() +
+    xlab("Clone Size") +
     ylab("Clonotype Bias")
-  if (exportTable == TRUE) { 
-    return(bias) 
-  }
-  return(plot) 
 }
 
 #Background summary of clones

R/clonalNetwork.R

@@ -204,6 +204,10 @@ clonalNetwork <- function(sc.data,
     V(graph)$size <- unname(clone.number)
     centers <- centers[rownames(centers) %in% names(V(graph)),]
 
+    if (exportTable) {
+      return(edge.list1)
+    }
+
     plot <- ggraph(graph, layout = centers[match(names(V(graph)), rownames(centers)),]) + 
                   geom_point(data = coord, aes(x = coord[,1], y = coord[,2], color = group.by)) + 
                   geom_edge_bend(aes(edge_color = as.numeric(weight)), 
@@ -228,9 +232,6 @@ clonalNetwork <- function(sc.data,
                       axis.line = element_line(colour = "black"), 
                       legend.key=element_blank()
                   )
-    if (exportTable) { 
-      return(edge.list1)
-    }
     return(plot)
 }
 

R/clonalRarefaction.R

@@ -61,11 +61,11 @@ clonalRarefaction <- function(input.data,
   })
   col <- length(input.data)
   mat <- iNEXT(mat.list, q=hill.numbers, datatype="abundance",nboot = n.boots) 
-  plot <- ggiNEXT(mat, type=plot.type)  + 
+  plot <- suppressMessages(ggiNEXT(mat, type=plot.type) + 
             scale_shape_manual(values = rep(16,col)) + 
             scale_fill_manual(values = rep("white", col)) + 
             scale_color_manual(values = c(.colorizer(palette,col)))  + 
-            theme_classic()
+            theme_classic())
   if (exportTable == TRUE) { 
     return(plot["data"]) 
   } else {

src/aaKmers.cpp

@@ -19,7 +19,7 @@ std::unordered_map<char, unsigned long int> allAaMap() {
 
 class AaKmerCounter {
 private:
-    // ideally these are all constants except bins
+    // ideally these are all constants except bins but this works :/
     std::unordered_map<unsigned long int, int> aaUIntKmerMap;
     int k;
     unsigned long int mask;