geom_striplab: geom_striplab

In GuangchuangYu/ggtree: an R package for visualization of tree and annotation data

geom_striplab

Description

annotate associated taxa (from taxa1 to taxa2, can be Monophyletic, Polyphyletic or Paraphyletc Taxa) with bar and (optional) text label or image

Usage

geom_striplab(
  taxa1 = NULL,
  taxa2 = NULL,
  label = NULL,
  data = NULL,
  mapping = NULL,
  geom = "text",
  parse = FALSE,
  ...
)

Arguments

taxa1	can be label or node number
taxa2	can be label or node number
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, default is NULL.
mapping	Set of aesthetic mappings, default is NULL. The detail see the following explanation.
geom	character, one of 'text', 'label', 'shadowtext', 'image' and 'phylopic', default is 'text', and the parameter see the Aesthetics For Specified Geom.
parse	logical, whether parse label to emoji font, default is 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, default is 0. offset.text distance bar and text, offset of text from bar, default is 0. align logical, whether align clade lab, default is FALSE. extend numeric, extend the length of bar, default is 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, default is 0. horizontal logical, whether set label to horizontal, default is TRUE. barsize the width of line, default is 0.5. barcolour the colour of line, default is 'black'. fontsize the size of text, default is 3.88. textcolour the colour of text, default is 'black'. imagesize the size of image, default is 0.05. imagecolor the colour of image, default is 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_striplab() understands the following aesthetics for geom="text"(required aesthetics are in bold):

• taxa1 selected tip label or tip node, it is required.

• taxa2 selected another tip label or tip node, it is required.

• label labels to be shown, it is required.

• colour the colour of text, default is "black".

• size the size of text, default is 3.88.

• angle the angle of text, default is 0.

• hjust A numeric vector specifying horizontal justification, default is 0.

• vjust A numeric vector specifying vertical justification, default is 0.5.

• alpha the transparency of text, default is NA.

• family the family of text, default is 'sans'.

• fontface the font face of text, default is 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, default is 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_striplab() understands the following aesthethics for geom="label" (required aesthetics are in bold):

• taxa1 selected node to hight light, it is required.

• taxa2 selected another tip label or tip node, it is required.

• label labels to be shown, it is required.

• colour the colour of text, default is "black".

• fill the background colour of the label, default is "white".

• size the size of text, default is 3.88.

• angle the angle of text, default is 0.

• hjust A numeric vector specifying horizontal justification, default is 0.

• vjust A numeric vector specifying vertical justification, default is 0.5.

• alpha the transparency of text, default is NA.

• family the family of text, default is 'sans'.

• fontface the font face of text, default is 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, default is 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_striplab() understands the following aesthethics for geom="shadowtext" (required aesthetics are in bold):

• taxa1 selected node to hight light, it is required.

• taxa2 selected another tip label or tip node, it is required.

• label labels to be shown, it is required.

• colour the colour of text, default is "black".

• bg.colour the background colour of text, default is 'black'.

• bg.r the width of background text, default is 0.1.

• size the size of text, default is 3.88.

• angle the angle of text, default is 0.

• hjust A numeric vector specifying horizontal justification, default is 0.

• vjust A numeric vector specifying vertical justification, default is 0.5.

• alpha the transparency of text, default is NA.

• family the family of text, default is 'sans'.

• fontface the font face of text, default is 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, default is 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_striplab() understands the following aesthethics for geom="image" or geom="phylopic" (required aesthetics are in bold):

• taxa1 selected node to hight light, it is required.

• taxa2 selected another tip label or tip node, 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, default is NULL.

• size the size of image, default is 0.05.

• alpha the alpha of image, default is 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(123)
tr <- rtree(10)
dt <- data.frame(ta1=c("t5", "t1"), ta2=c("t6", "t3"), group=c("A", "B"))
p <- ggtree(tr) + geom_tiplab()
p2 <- p + 
      geom_striplab(
        data = dt,
        mapping = aes(taxa1 = ta1, taxa2 = ta2, 
                      label = group, color=group),
        align = TRUE,
        show.legend = FALSE
      )
p2

GuangchuangYu/ggtree documentation built on Oct. 31, 2024, 10:10 a.m.