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

Description Usage Arguments Aesthetics For Specified Geom Examples

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

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

`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, 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.

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 showed, 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_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 showed, 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_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 showed, 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_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 showed, 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.

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, 
                             offset.text=offset.text),
                        geom="shadowtext",
                        hjust=0.5,
                        align=TRUE,
                        horizontal=FALSE,
                        angle=90
                       ) 
p2

Registered S3 method overwritten by 'treeio':
  method     from
  root.phylo ape 
ggtree v2.4.1  For help: https://yulab-smu.top/treedata-book/

If you use ggtree in published research, please cite the most appropriate paper(s):

[36m-[39m Guangchuang Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics, 2020, 69:e96. doi:10.1002/cpbi.96
[36m-[39m Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution 2018, 35(12):3041-3043. doi:10.1093/molbev/msy194
[36m-[39m Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36. doi:10.1111/2041-210X.12628


Loading required package: shadowtext
Warning message:
Removed 2 rows containing missing values (geom_shadow_text).