Allow use of scattermore/scattermost in plotPairs

Author: csoneson

DESCRIPTION

@@ -55,7 +55,8 @@ Suggests:
     knitr,
     Biostrings,
     pwalign,
-    plotly
+    plotly,
+    scattermore
 SystemRequirements: GNU make
 biocViews: GeneticVariability, GenomicVariation, Preprocessing
 License: MIT + file LICENSE

NEWS.md

@@ -1,3 +1,7 @@
+# mutscan 0.3.4
+
+* Allow use of scattermore/scattermost in plotPairs
+
 # mutscan 0.3.3
 
 * Bugfix in mergeReadPairPartial for situation where specified minMergedLength/maxMergedLength is larger than the total length of the two merged sequences

R/plotPairs.R

@@ -23,8 +23,9 @@
 #'     to calculate.
 #' @param histBreaks Numeric scalar, the number of breaks in the histograms
 #'     to put in the diagonal panels.
-#' @param pointsType Either "points" or "smoothscatter", determining the
-#'     type of plots that will be made.
+#' @param pointsType Either "points", "smoothscatter", "scattermore" or 
+#'     "scattermost" (the latter two require the "scattermore" package to be 
+#'     installed), determining the type of plots that will be made.
 #' @param corSizeMult,corSizeAdd Numeric scalars determining how the
 #'     absolute correlation value is transformed into a font size. The
 #'     transformation is corSizeMult * abs(corr) + corSizeAdd.
@@ -71,7 +72,8 @@ plotPairs <- function(se, selAssay = "counts", doLog = TRUE, pseudocount = 1,
                   validValues = c("pearson", "spearman"))
     .assertScalar(x = histBreaks, type = "numeric", rngExcl = c(0, Inf))
     .assertScalar(x = pointsType, type = "character",
-                  validValues = c("smoothscatter", "points"))
+                  validValues = c("smoothscatter", "points", "scattermore",
+                                  "scattermost"))
     .assertScalar(x = corSizeMult, type = "numeric", rngExcl = c(0, Inf))
     .assertScalar(x = corSizeAdd, type = "numeric", rngIncl = c(0, Inf))
     .assertScalar(x = pointSize, type = "numeric", rngExcl = c(0, Inf))
@@ -83,6 +85,9 @@ plotPairs <- function(se, selAssay = "counts", doLog = TRUE, pseudocount = 1,
         stopifnot(corrColorRange[2] >= corrColorRange[1])
     }
     .assertScalar(x = addIdentityLine, type = "logical")
+    if (pointsType %in% c("scattermore", "scattermost")) {
+        .assertPackagesAvailable("scattermore")
+    }
 
     ## ----------------------------------------------------------------------- ##
     ## Define shared theme elements
@@ -168,11 +173,61 @@ plotPairs <- function(se, selAssay = "counts", doLog = TRUE, pseudocount = 1,
         }
     }
 
+    ## Define function to create scattermore plot (for use with ggpairs)
+    if (addIdentityLine) {
+        plotscattermore <- function(data, mapping, ...) {
+            ggplot2::ggplot(data = data, mapping = mapping) +
+                ggplot2::geom_abline(slope = 1, intercept = 0, 
+                                     linetype = "dashed", color = "grey") + 
+                scattermore::geom_scattermore(alpha = pointAlpha, 
+                                              pointsize = pointSize) +
+                ggtheme
+        }
+    } else {
+        plotscattermore <- function(data, mapping, ...) {
+            ggplot2::ggplot(data = data, mapping = mapping) +
+                scattermore::geom_scattermore(alpha = pointAlpha, 
+                                              pointsize = pointSize) +
+                ggtheme
+        }
+    }
+    
+    ## Define function to create scattermost plot (for use with ggpairs)
+    if (addIdentityLine) {
+        plotscattermost <- function(data, mapping, ...) {
+            ## Get data
+            xData <- GGally::eval_data_col(data, mapping$x)
+            yData <- GGally::eval_data_col(data, mapping$y)
+            
+            ggplot2::ggplot(data = data, mapping = mapping) +
+                ggplot2::geom_abline(slope = 1, intercept = 0, 
+                                     linetype = "dashed", color = "grey") + 
+                scattermore::geom_scattermost(xy = cbind(xData, yData), 
+                                              pointsize = pointSize) +
+                ggtheme
+        }
+    } else {
+        plotscattermost <- function(data, mapping, ...) {
+            ## Get data
+            xData <- GGally::eval_data_col(data, mapping$x)
+            yData <- GGally::eval_data_col(data, mapping$y)
+            
+            ggplot2::ggplot(data = data, mapping = mapping) +
+                scattermore::geom_scattermost(xy = cbind(xData, yData), 
+                                              pointsize = pointSize) +
+                ggtheme
+        }
+    }
+    
     ## Define the function to use for the plots
     if (pointsType == "smoothscatter") {
         lower <- list(continuous = smoothscat)
     } else if (pointsType == "points") {
         lower <- list(continuous = plotpoints)
+    } else if (pointsType == "scattermore") {
+        lower <- list(continuous = plotscattermore)
+    } else if (pointsType == "scattermost") {
+        lower <- list(continuous = plotscattermost)
     }
 
     ## ----------------------------------------------------------------------- ##