Helper to specify a HeatmapAnnotation for taxa

Usage

taxAnnotation(
  ...,
  name,
  annotation_legend_param = list(),
  show_legend = TRUE,
  gp = grid::gpar(col = NA),
  border = FALSE,
  gap = grid::unit(2, "mm"),
  show_annotation_name = TRUE,
  annotation_label = NULL,
  annotation_name_gp = grid::gpar(),
  annotation_name_offset = NULL,
  annotation_name_rot = NULL,
  annotation_name_align = TRUE,
  annotation_name_side = "auto",
  .data = NULL,
  .taxa = NULL,
  .side = NULL
)

Arguments

...: Name-value pairs where the names correspond to annotation names and values are the output of taxon annotation functions such as anno_tax_prev() or manually specified AnnotationFunction objects
name: Name of the heatmap annotation, optional.
annotation_legend_param: A list which contains parameters for annotation legends. See color_mapping_legend,ColorMapping-method for all possible options.
show_legend: Whether show annotation legends. The value can be one single value or a vector.
gp: Graphic parameters for simple annotations (with fill parameter ignored).
border: border of single annotations.
gap: Gap between annotations. It can be a single value or a vector of unit objects.
show_annotation_name: Whether show annotation names? For column annotation, annotation names are drawn either on the left or the right, and for row annotations, names are draw either on top or at the bottom. The value can be a vector.
annotation_label: Labels for the annotations. By default it is the same as individual annotation names.
annotation_name_gp: Graphic parameters for annotation names. Graphic parameters can be vectors.
annotation_name_offset: Offset to the annotation names, a unit object. The value can be a vector.
annotation_name_rot: Rotation of the annotation names. The value can be a vector.
annotation_name_align: Whether to align the annotation names.
annotation_name_side: Side of the annotation names.
.data: OPTIONAL phyloseq or psExtra, only set this to override use of same data as in heatmap
.taxa: OPTIONAL selection vector of taxa (names, numbers or logical), only set this if providing .data argument to override default
.side: OPTIONAL string, indicating the side the taxa annotation should be placed: only set this to override default

Value

HeatmapAnnotation object

Examples

library("ComplexHeatmap")
data("ibd", package = "microViz")
psq <- tax_filter(ibd, min_prevalence = 5)
psq <- tax_mutate(psq, Species = NULL)
psq <- tax_fix(psq)
psq <- tax_agg(psq, rank = "Family")
taxa <- tax_top(psq, n = 15, rank = "Family")

customAxis <- list(labels_rot = 0, at = c(0, 0.5, 1))

# makes a function that takes data, taxa and which (at minimum)
fun <- taxAnnotation(
  gap = grid::unit(2.5, "mm"),
  Prev. = anno_tax_prev(axis_param = customAxis, ylim = c(0, 1), extend = 0),
  `Prop. Abd.` = anno_tax_box(size = unit(40, "mm"), axis_param = customAxis),
  `Log10p Abd.` = anno_tax_density(type = "heatmap")
)

# manually specify the prevalence barplot function by giving it data etc.
heatmapAnnoFunction <- fun(.data = psq, .side = "top", .taxa = taxa)

# draw the annotation without a heatmap, you will never normally do this!
grid.newpage()
vp <- viewport(width = 0.65, height = 0.75)
pushViewport(vp)
draw(heatmapAnnoFunction)


# try again as a row annotation
grid.newpage()
pushViewport(vp)
draw(fun(.data = psq, .side = "right", .taxa = rev(taxa)))