geom_tiplab: geom_tiplab

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

geom_tiplab

Description

add tip label layer for a tree

Usage

geom_tiplab(
  mapping = NULL,
  hjust = 0,
  align = FALSE,
  linetype = "dotted",
  linesize = 0.5,
  geom = "text",
  offset = 0,
  as_ylab = FALSE,
  ...
)

Arguments

mapping	aes mapping
hjust	horizontal adjustment, defaults to 0
align	if TRUE, align all tip labels to the longest tip by adding padding characters to the left side of tip labels, defaults to "FALSE" with a line connecting each tip and its corresponding label, defaults to "FALSE"
linetype	set linetype of the line if align = TRUE, defaults to "dotted"
linesize	set line width if align = TRUE, defaults to 0.5
geom	one of 'text', 'label', 'shadowtext', 'image' and 'phylopic'
offset	tiplab offset, horizontal adjustment to nudge tip labels, defaults to 0
as_ylab	display tip labels as y-axis label, only works for rectangular and dendrogram layouts, defaults to "FALSE"
...	additional parameter additional parameters can refer the following parameters. The following parameters for geom="text". size control the size of tip labels, defaults to 3.88. colour control the colour of tip labels, defaults to "black". angle control the angle of tip labels, 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 . nudge_x horizontal adjustment to nudge labels, defaults to 0. nudge_y vertical adjustment to nudge labels, defaults to 0. check.overlap if TRUE, text that overlaps previous text in the same layer will not be plotted. parse if TRUE, the labels will be parsed into expressions, if it is 'emoji', the labels will be parsed into emojifont. The following parameters for geom="label". size the size of tip labels, defaults to 3.88. colour the colour of tip labels, defaults to "black". fill the colour of rectangular box of labels, defaults to "white". vjust numeric vector specifying vertical justification, defaults to 0.5. alpha the transparency of labels, 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. nudge_x horizontal adjustment to nudge labels, defaults to 0. nudge_y vertical adjustment, defaults to 0. check.overlap if TRUE, text that overlaps previous text in the same layer will not be plotted. parse if TRUE, the labels will be parsed into expressions, if it is 'emoji', the labels will be parsed into emojifont. label.padding Amount of padding around label, defaults to 'unit(0.25, "lines")'. label.r Radius of rounded corners, defaults to 'unit(0.15, "lines")'. label.size Size of label border, in mm, defaults to 0.25. The following parameters for geom="shadowtext", some parameters are like to geom="text". bg.colour the background colour of text, defaults to "black". bg.r the width of background of text, defaults to 0.1 . The following parameters for geom="image" or geom="phylopic". image the image file path for geom='image', but when geom='phylopic', it should be the uid of phylopic databases. size the image size, defaults to 0.05. colour the color of image, defaults to NULL. alpha the transparency of image, defaults to 0.8. The following parameters for the line when align = TRUE. colour the colour of line, defaults to 'black'. alpha the transparency of line, defaults to NA. arrow specification for arrow heads, as created by arrow(), defaults to NULL. arrow.fill fill color to usse for the arrow head (if closed), defaults to 'NULL', meaning use 'colour' aesthetic.

Details

'geom_tiplab' not only supports using text or label geom to display tip labels, but also supports image geom to label tip with image files or phylopics.

For adding tip labels to a tree with circular layout, 'geom_tiplab' will automatically adjust the angle of the tip labels to the tree by internally calling 'geom_tiplab2'.

Value

tip label layer

Author(s)

Guangchuang Yu

References

For more detailed demonstration, please refer to chapter 4.3.3 of Data Integration, Manipulation and Visualization of Phylogenetic Trees http://yulab-smu.top/treedata-book/index.html by Guangchuang Yu.

Examples

require(ape)
tr <- rtree(10)
ggtree(tr) + geom_tiplab()

YuLab-SMU/ggtree documentation built on Nov. 3, 2024, 4:15 p.m.