R/variant_scales.R

In thackl/gggenomes: A Grammar of Graphics for Comparative Genomics

#' Default colors and shapes for mutation types.
#'
#' @description 
#' The user can call upon an convenient function called `scale_color_variant`,
#' which changes the color of (SNP) points, based on their nucleotides (A, C, G, T).
#' By default the function uses a colorblind friendly palette, but users can manually overwrite these colors.     
#' *(Within the plotting function (e.g. `geom_variant`), coloring of the column should still be mentioned (`aes(color = ...)`).*     
#'  
#' The function `scale_shape_variant` changes the shape of plotted points based on the type of mutation.
#' The user can also manually decide which shape, each specific type of mutation should have.
#' By default, SNPs are diamond shaped, Deletions triangle downwards and Insertions triangle upwards.
#' (These default settings make most sense when using `geom_variant(offset = -0.2)`).      
#' *(User should still manually call which column is used for the shape aesthetic)*
#'   
#' @param values A vector indicating how to color/shape different variables. 
#' The functions `scale_color_variant()` and `scale_shape_variant()` have a default setting, which can be overwritten.
#' @param na.value The aesthetic value (color/shape/etc.) to use for non matching values.
#' @param characters When `TRUE`, it changes the default shapes of `scale_shape_variant()` to become the letters of the nucleotides.
#' @param ... Additional parameters, passed to scale_color_manual
#' @export
#' @examples 
#' # Creation of example data. 
#' testposition <- tibble::tibble(
#' type = c("Insertion", "SNP", "SNP", "Deletion",
#'   "Deletion", "SNP", "SNP", "Insertion", "SNP", "Insertion", "SNP"),
#' start = c(10, 20, 30, 35, 40, 60, 65, 90, 90, 100, 120),
#' ALT = c("AT", "G", "C", ".", ".", "T", "C", "CAT", "G", "TC", "A"),
#' REF = c("A", "T", "G", "A", "A", "G", "A", "C", "A", "T", "G"),
#' end = start + 1,
#' seq_id = c(rep("A", 11)))
#' 
#' testseq <- tibble::tibble(
#' seq_id = "A",
#' start = 0,
#' end = 150,
#' length = end-start)
#' 
#' p1 <- gggenomes(seqs=testseq, feats=testposition)
#' p2 <- p1 + geom_seq()
#'
#' ## Scale_color_variant()
#' # Changing the color aesthetics in geom_variant: colors all mutations
#' # (In this example, All ALT (alternative) nucleotides are being colored)
#' p1 + geom_variant(aes(color=ALT)) 
#' 
#' # Color all SNPs with default colors using scale_color_variant().
#' #(SNPs are 1 nucleotide long, other mutations such as Insertions
#' #and Deletions have either more ore less nucleotides within the
#' #ALT column and are thus not plotted)
#' p1 + geom_variant(aes(color=ALT)) +
#' scale_color_variant()
#' 
#' # Manually changing colors with scale_color_variant()
#' p1 + geom_variant(aes(color=ALT)) +
#' scale_color_variant(values = c(A="purple", T="darkred", TC="black", AT="pink"))
#'
#' ## Scale_shape_variant()
#' # Changing the `shape` aesthetics in geom_variant
#' p2 + geom_variant(aes(shape=type), offset = -0.1)
#' 
#' # Calling upon scale_shape_variant() to change shapes
#' p2 + geom_variant(aes(shape=type), offset = -0.1) +
#' scale_shape_variant()
#' 
#' # Manually changing shapes with scale_shape_variant()
#' p2 + geom_variant(aes(shape=type), offset = -0.1) +
#' scale_shape_variant(values=c(SNP=14, Deletion=18, Insertion=21))
#' 
#' # Plotting (nucleotides) characters instead of shapes
#' p2 + geom_variant(aes(shape=ALT), offset = -0.1, size=3)+
#' scale_shape_variant(characters=TRUE)
#' 
#' # Alternative way to plot nucleotides (of ALT) by using `geom=text` within `geom_variant()`
#'  gggenomes(seqs=testseq, feats=testposition) +
#'  geom_seq() +
#'  geom_variant(aes(shape=type), offset=-0.1) +
#'  scale_shape_variant() +
#'  geom_variant(aes(label=ALT), geom="text", offset=-0.25) +
#'  geom_bin_label()  
#' 
#' # Combining scale_color_variant() and scale_shape_variant()
#' p2 + geom_variant(aes(shape=ALT, color = ALT), offset = -0.1, size = 3, show.legend=FALSE) +
#' geom_variant(aes(color=ALT)) +
#' scale_color_variant(na.value = "black") +
#' scale_shape_variant(characters=TRUE)
#'
# The function scale_color_variant is used to get the correct shape for each kind of mutation
scale_color_variant <- function(values = c(A="#e66101", C="#b2abd2", G="#5e3c99", T="#fdb863"), na.value = "white", ...){
                                scale_color_manual(values = values, na.value = na.value, ...)}

#' @rdname scale_color_variant
#' @export
# The function scale_shape_variant is used to get the correct shape for each kind of mutation
scale_shape_variant <- function(values=c(SNP=23, Deletion=25, Insertion=24), na.value = 1, characters = FALSE, ...){
  if(characters){values <- c(A=65, C=67, G=71, T= 84)}
  scale_shape_manual(values=values, ...)}