View source: R/geom_cladelab.R
geom_cladelab | R Documentation |
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, 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.
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 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.
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
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