Description Usage Arguments Details Examples
Shows a diagram of an annotated heatmap layout for given specification.
1 | aheatmap_layout(layout = "daml", size = NULL)
|
layout |
layout specification that indicates the relative position of the heatmap's components. Two layouts can be defined: one horizontal, which relates to components associated to rows, and one vertical, which relates to components associated with columns. Each layout is specified as a character strings, composed of characters that encode the order of each component: dendrogram (d), annotation tracks (a), data matrix (m), labels (l) and legend (L). See section Layout syntax for a complete specification |
size |
list defining the size of each component (mainly for internal use). |
Layout syntax:
Layouts are specified as character strings that can contain the following characters, each associated with a given component or behaviour:
Components
dendrogram component
annotation tracks
data matrix
labels
scale legend
Behaviours
align top (resp. left) for horizontal (resp. vertical) layout.
align middle (resp. center) for horizontal (resp. vertical) layout.
align bottom (resp. right) for horizontal (resp. vertical) layout.
If used alone (i.e. layout = "_"
), then this is equivalent to "|.L_"
,
which places the legend horizontally on the bottom-right corner.
used either alone or after after ‘L’ to specifiy that the legend should expand to full height/width.
The specification must contain one instance of each of these character.
The default horizontal/vertical layout is "daml"
, and can also be specified
as "."
.
Separate layouts can be passed as a character vector with 2 element (e.g., c("daml", "mald")
),
or as a single string, with layouts separated by "|"
(e.g., "almd | L."
).
When using this separator, a layout specification may be omitted, indicating
that the default layout shoud be used: "almd|"
is equivalent to "almd | ."
.
If only one layout specification is passed (i.e. a string without "|"
),
then it is used for both horizontal and vertical layouts.
Shortcuts
layout = "*"
is a shortcut for layout = ".L*"
, which expands the legend to
take up full height;
layout = "_"
is a shortcut for layout = "|.L_"
, which puts the legend at
bottom-right corner;
layout = "_^"
is a shortcut for layout = "|.L^"
, which puts the legend at
bottom-left corner;
layout = "_*"
is a shortcut for layout = "|.L*"
, which puts the legend
at bottom, expanded to take up full width;
layout = "^"
is a shortcut for layout = "L^.|"
, which puts the legend
on the top-left corner.
Examples:
layout = "dlma"
puts labels at the leaves of the dendrograms and
annotation track below or at the right of the data matrix
layout = ". | amld"
use the default layout for rows, put
column annotation track on top of the data matrix, followed by column labels and
dendrogram.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | # default layout
aheatmap_layout()
# Common row/column layout: annotations > data > labels > dendrogram
aheatmap_layout('amld')
# Separate row/column layout: row as above / column as default
aheatmap_layout('amld | .')
## Legend
# horizontal bottom-right
aheatmap_layout('_')
# hotizontal top-left (equivalent to "|L^.")
aheatmap_layout('^')
|
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