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Helper to specify a HeatmapAnnotation for samples in comp_heatmap

Source: R/heatmaps-sampleAnnotation.R
sampleAnnotation.Rd

Helper to specify a HeatmapAnnotation for samples in comp_heatmap

Usage

sampleAnnotation(
  ...,
  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 = FALSE,
  annotation_name_side = "auto",
  .data = NULL,
  .samples = NULL,
  .side = NULL
)

Arguments

...

Name-value pairs where the names correspond to annotation names and values are the output of sample annotation functions such as anno_sample(), 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

.samples

OPTIONAL selection vector of sample names, only set this if providing .data argument to override default

.side

OPTIONAL string, indicating the side for the variable annotations: only set this to override default

Value

HeatmapAnnotation object

See also

taxAnnotation()

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")
samples <- phyloseq::sample_names(psq)

set.seed(42) # random colours used in first example
# sampleAnnotation returns a function that takes data, samples, and which
fun <- sampleAnnotation(
  gap = grid::unit(2.5, "mm"),
  Dis1 = anno_sample(var = "DiseaseState"),
  IBD = anno_sample_cat(var = "ibd"),
  Dis2 = anno_sample_cat(var = "DiseaseState", col = 1:4)
)

# manually specify the sample annotation function by giving it data etc.
heatmapAnnoFunction <- fun(.data = psq, .side = "top", .samples = samples)

# 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)
pushViewport(viewport(x = 0.7, y = 0.6))
draw(attr(heatmapAnnoFunction, "Legends"))