geom_cladelab: geom_cladelab

In YuLab-SMU/ggtree: an R package for visualization of tree and annotation data

geom_cladelab

Description

annotate a clade with bar and text label or (image)

Usage

geom_cladelab(
  node = NULL,
  label = NULL,
  data = NULL,
  mapping = NULL,
  geom = "text",
  parse = FALSE,
  ...
)

Arguments

node	selected node to annotate, when data and mapping is NULL, it is required.
label	character, character to be showed, when data and mapping is NULL, it is required.
data	data.frame, the data to be displayed in the annotation, defaults to NULL.
mapping	Set of aesthetic mappings, defaults to NULL. The detail see the following explanation.
geom	character, one of 'text', 'label', 'shadowtext', 'image' and 'phylopic', defaults to 'text', and the parameter see the Aesthetics For Specified Geom.
parse	logical, whether parse label to emoji font, defaults to FALSE.
...	additional parameters, see also following section. additional parameters can refer the following parameters. offset distance bar and tree, offset of bar and text from the clade, defaults to 0. offset.text distance bar and text, offset of text from bar, defaults to 0. align logical, whether align clade lab, defaults to FALSE. extend numeric, extend the length of bar, defaults to 0. angle numeric or 'auto', if angle is auto, the angle of text will be calculated automatically, which is useful for the circular etc layout, defaults to 0. horizontal logical, whether set label to horizontal, defaults to TRUE. barsize the width of line, defaults to 0.5. barcolour the colour of line, defaults to 'black'. fontsize the size of text, defaults to 3.88. textcolour the colour of text, defaults to 'black'. imagesize the size of image, defaults to 0.05. imagecolor the colour of image, defaults to NULL, when geom="phylopic", it should be required. The parameters also can be set in mapping, when data is provided. Note: the barsize, barcolour, fontsize, textcolour, imagesize and imagecolor should not be set in mapping (aesthetics). When the color and size are not be set in mapping, user can modify them to adjust the attributes of specified geom.

Aesthetics For Specified Geom

geom_cladelab() understands the following aesthetics for geom="text"(required aesthetics are in bold):

• node selected node to hight light, it is required.

• label labels to be shown, it is required.

• colour the colour of text, defaults to "black".

• size the size of text, defaults to 3.88.

• angle the angle of text, defaults to 0.

• hjust A numeric vector specifying horizontal justification, defaults to 0.

• vjust A numeric vector specifying vertical justification, defaults to 0.5.

• alpha the transparency of text, defaults to NA.

• family the family of text, defaults to 'sans'.

• fontface the font face of text, defaults to 1 (plain), others are 2 (bold), 3 (italic), 4 (bold.italic).

• lineheight The height of a line as a multiple of the size of text, defaults to 1.2 .

when the colour, size are not be set in mapping, and user want to modify the colour of text, they should use textcolour, fontsize to avoid the confusion with bar layer annotation.

geom_cladelab() understands the following aesthethics for geom="label" (required aesthetics are in bold):

• node selected node to hight light, it is required.

• label labels to be shown, it is required.

• colour the colour of text, defaults to "black".

• fill the background colour of the label, defaults to "white".

• size the size of text, defaults to 3.88.

• angle the angle of text, defaults to 0.

• hjust A numeric vector specifying horizontal justification, defaults to 0.

• vjust A numeric vector specifying vertical justification, defaults to 0.5.

• alpha the transparency of text, defaults to NA.

• family the family of text, defaults to 'sans'.

• fontface the font face of text, defaults to 1 (plain), others are 2 (bold), 3 (italic), 4 (bold.italic).

• lineheight The height of a line as a multiple of the size of text, defaults to 1.2 .

when the colour, size are not be set in mapping, and user want to modify the colour of text, they should use textcolour, fontsize to avoid the confusion with bar layer annotation.

geom_cladelab() understands the following aesthethics for geom="shadowtext" (required aesthetics are in bold):

• node selected node to hight light, it is required.

• label labels to be shown, it is required.

• colour the colour of text, defaults to "black".

• bg.colour the background colour of text, defaults to 'black'.

• bg.r the width of background text, defaults to 0.1.

• size the size of text, defaults to 3.88.

• angle the angle of text, defaults to 0.

• hjust A numeric vector specifying horizontal justification, defaults to 0.

• vjust A numeric vector specifying vertical justification, defaults to 0.5.

• alpha the transparency of text, defaults to NA.

• family the family of text, defaults to 'sans'.

• fontface the font face of text, defaults to 1 (plain), others are 2 (bold), 3 (italic), 4 (bold.italic).

• lineheight The height of a line as a multiple of the size of text, defaults to 1.2 .

when the colour, size are not be set in mapping, and user want to modify the colour of text, they should use textcolour, fontsize to avoid the confusion with bar layer annotation.

geom_cladelab() understands the following aesthethics for geom="image" or geom="phylopic" (required aesthetics are in bold):

• node selected node to hight light, it is required.

• label labels to be shown, it is required.

• image the image to be annotated, when geom="phylopic", the uid of phylopic databases, it is required.

• colour the color of image, defaults to NULL.

• size the size of image, defaults to 0.05.

• alpha the alpha of image, defaults to 0.8.

when the colour, size are not be set in mapping, and user want to modify the colour of image, they should use imagecolour, imagesize to avoid the confusion with bar layer annotation.

Examples

set.seed(2015-12-21)
tree <- rtree(30)
data <- data.frame(id=c(34, 56),
                   annote=c("another clade", "long clade names"),
                   image=c("7fb9bea8-e758-4986-afb2-95a2c3bf983d",
                           "0174801d-15a6-4668-bfe0-4c421fbe51e8"),
                   group=c("A", "B"),
                   offset=c(0.1, 0.1),
                   offset.text=c(0.1, 0.2))

p <- ggtree(tree) + xlim(NA, 6)

p + geom_cladelab(node=45, label="test label") +
    geom_cladelab(node=34, label="another clade")
p2 <- p + geom_cladelab(data=data,
                        mapping=aes(
                             node=id, 
                             label=annote, 
                             image=image,
                             color=group, 
                             offset=offset
                        ),
                        geom="shadowtext",
                        hjust=0.5,
                        align=TRUE,
                        horizontal=FALSE,
                        angle=90,
                        show.legend = FALSE
                       ) 
p2

YuLab-SMU/ggtree documentation built on April 15, 2024, 5:19 p.m.