Include col argument in residual plotting functions

amvillegas · Feb 9, 2016 · 0e3260f · 0e3260f
1 parent 4c48aaf
commit 0e3260f
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Showing 4 changed files with 20 additions and 7 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -48,7 +48,6 @@ importFrom(graphics,image.default)
 importFrom(graphics,lines)
 importFrom(graphics,par)
 importFrom(graphics,plot)
-importFrom(methods,hasArg)
 importFrom(rootSolve,multiroot)
 importFrom(stats,aggregate)
 importFrom(stats,as.formula)

diff --git a/R/docStMoMo.R b/R/docStMoMo.R
@@ -16,7 +16,6 @@
 #' @importFrom stats rpois runif start
 #' @importFrom utils head tail
 #' @importFrom RColorBrewer brewer.pal
-#' @importFrom methods hasArg 
 NULL
 
 

diff --git a/R/residualsfitStMoMo.R b/R/residualsfitStMoMo.R
@@ -67,7 +67,7 @@ residuals.fitStMoMo <- function(object, scale = TRUE, ...) {
 #'                                             "signplot"), 
 #'                                 reslim = NULL, plotAge = TRUE, 
 #'                                 plotYear = TRUE, plotCohort  = TRUE, 
-#'                                 pch = 20, ...)
+#'                                 pch = 20, col = NULL, ...)
 #' 
 #' @param x an object of class \code{resStMoMo} with the residuals of a 
 #' Stochastic Mortality Model.
@@ -84,6 +84,11 @@ residuals.fitStMoMo <- function(object, scale = TRUE, ...) {
 #' @param pch optional symbol to use for the points in a scatterplot. 
 #' This is only used when \code{type = "scatter"}. See 
 #' \code{\link[graphics]{plot}}.
+#' @param col optional colours to use in plotting. If 
+#' \code{type = "scatter"} this is a single colour to use in the points
+#' in the scatter plots, while if \code{type = "colourmap"} this should
+#' be a list of colours (see help in \code{\link[fields]{image.plot}} 
+#' for details). This argument is ignored if \code{type = "signplot"}.
 #' @param ... other plotting parameters to be passed to the plotting 
 #' functions. This can be used to control the appearance of the plots.
 #'
@@ -116,23 +121,27 @@ residuals.fitStMoMo <- function(object, scale = TRUE, ...) {
 #' @method plot resStMoMo
 plot.resStMoMo <- function(x, type = c("scatter", "colourmap", "signplot"), 
                            reslim = NULL, plotAge = TRUE, plotYear = TRUE, 
-                           plotCohort  = TRUE, pch = 20, ...) {
+                           plotCohort  = TRUE, pch = 20, col = NULL, ...) {
   type <- match.arg(type)
   oldpar <- par(no.readonly = TRUE)
 
   if (is.null(reslim)) {
     maxRes <- max(abs(x$residuals), na.rm = TRUE)
     reslim <- c(-maxRes, maxRes)
   }
-  if (!hasArg(col)) {
+  if (is.null(col) & type == "colourmap") {
     col <- colorRampPalette(RColorBrewer::brewer.pal(10, "RdBu"))(64)
   }
+  if (is.null(col) & type == "scatter") {
+    col <- "black"
+  }
 
   switch(type, 
          scatter = scatterplotAPC(x$residuals, x$ages, x$years, 
                                   plotAge = plotAge, plotYear = plotYear, 
                                   plotCohort = plotCohort, pch = pch, 
-                                  ylab = "residuals", ylim = reslim, ...),
+                                  ylab = "residuals", ylim = reslim, 
+                                  col = col, ...),
          colourmap = fields::image.plot(x$year, x$age, t(x$residuals), 
                                         zlim = reslim, ylab = "age", 
                                         xlab = "calendar year", col = col, 

diff --git a/man/plot.resStMoMo.Rd b/man/plot.resStMoMo.Rd
@@ -8,7 +8,7 @@
                                             "signplot"),
                                 reslim = NULL, plotAge = TRUE,
                                 plotYear = TRUE, plotCohort  = TRUE,
-                                pch = 20, ...)
+                                pch = 20, col = NULL, ...)
 }
 \arguments{
 \item{x}{an object of class \code{resStMoMo} with the residuals of a
@@ -33,6 +33,12 @@ should be produced. This is only used when \code{type = "scatter"}.}
 This is only used when \code{type = "scatter"}. See
 \code{\link[graphics]{plot}}.}
 
+\item{col}{optional colours to use in plotting. If
+\code{type = "scatter"} this is a single colour to use in the points
+in the scatter plots, while if \code{type = "colourmap"} this should
+be a list of colours (see help in \code{\link[fields]{image.plot}}
+for details). This argument is ignored if \code{type = "signplot"}.}
+
 \item{...}{other plotting parameters to be passed to the plotting
 functions. This can be used to control the appearance of the plots.}
 }