The functions below are useful for labeling features/genes in plots.
Users have to call on aes(label = ...)
or (label = ...)
to define label's text
Based on the function, the label will be placed at a specific location:
geom_..._text()
will plot text in the middle of the feature.
geom_..._tag()
will plot text on top of the feature, with a 45 degree angle.
geom_..._note()
will plot text under the feature at the left side.
The ...
can be either replaced with feat
or gene
depending on which
track the user wants to label.
With arguments such as hjust
, vjust
, angle
, and nudge_y
, the user
can also manually change the position of the text.
geom_feat_text(
mapping = NULL,
data = feats(),
stat = "identity",
position = "identity",
...,
parse = FALSE,
check_overlap = FALSE,
na.rm = FALSE,
show.legend = NA,
inherit.aes = TRUE
)
geom_feat_tag(
mapping = NULL,
data = feats(),
stat = "identity",
position = "identity",
hjust = 0,
vjust = 0,
angle = 45,
nudge_y = 0.03,
xjust = 0.5,
strandwise = TRUE,
...,
parse = FALSE,
check_overlap = FALSE,
na.rm = FALSE,
show.legend = NA,
inherit.aes = TRUE
)
geom_feat_note(
mapping = NULL,
data = feats(),
stat = "identity",
position = "identity",
hjust = 0,
vjust = 1,
nudge_y = -0.03,
xjust = 0,
strandwise = FALSE,
...,
parse = FALSE,
check_overlap = FALSE,
na.rm = FALSE,
show.legend = NA,
inherit.aes = TRUE
)
geom_gene_text(
mapping = NULL,
data = genes(),
stat = "identity",
position = "identity",
...,
parse = FALSE,
check_overlap = FALSE,
na.rm = FALSE,
show.legend = NA,
inherit.aes = TRUE
)
geom_gene_tag(
mapping = NULL,
data = genes(),
stat = "identity",
position = "identity",
hjust = 0,
vjust = 0,
angle = 45,
nudge_y = 0.03,
xjust = 0.5,
strandwise = TRUE,
...,
parse = FALSE,
check_overlap = FALSE,
na.rm = FALSE,
show.legend = NA,
inherit.aes = TRUE
)
geom_gene_note(
mapping = NULL,
data = genes(),
stat = "identity",
position = "identity",
hjust = 0,
vjust = 1,
nudge_y = -0.03,
xjust = 0,
strandwise = FALSE,
...,
parse = FALSE,
check_overlap = FALSE,
na.rm = FALSE,
show.legend = NA,
inherit.aes = TRUE
)
Set of aesthetic mappings created by aes()
. If specified and
inherit.aes = TRUE
(the default), it is combined with the default mapping
at the top level of the plot. You must supply mapping
if there is no plot
mapping.
The data to be displayed in this layer. There are three options:
If NULL
, the default, the data is inherited from the plot
data as specified in the call to ggplot()
.
A data.frame
, or other object, will override the plot
data. All objects will be fortified to produce a data frame. See
fortify()
for which variables will be created.
A function
will be called with a single argument,
the plot data. The return value must be a data.frame
, and
will be used as the layer data. A function
can be created
from a formula
(e.g. ~ head(.x, 10)
).
The statistical transformation to use on the data for this
layer, either as a ggproto
Geom
subclass or as a string naming the
stat stripped of the stat_
prefix (e.g. "count"
rather than
"stat_count"
)
Position adjustment, either as a string, or the result of
a call to a position adjustment function. Cannot be jointly specified with
nudge_x
or nudge_y
.
Other arguments passed on to layer()
. These are
often aesthetics, used to set an aesthetic to a fixed value, like
colour = "red"
or size = 3
. They may also be parameters
to the paired geom/stat.
If TRUE
, the labels will be parsed into expressions and
displayed as described in ?plotmath
.
If TRUE
, text that overlaps previous text in the
same layer will not be plotted. check_overlap
happens at draw time and in
the order of the data. Therefore data should be arranged by the label
column before calling geom_text()
. Note that this argument is not
supported by geom_label()
.
If FALSE
, the default, missing values are removed with
a warning. If TRUE
, missing values are silently removed.
logical. Should this layer be included in the legends?
NA
, the default, includes if any aesthetics are mapped.
FALSE
never includes, and TRUE
always includes.
It can also be a named logical vector to finely select the aesthetics to
display.
If FALSE
, overrides the default aesthetics,
rather than combining with them. This is most useful for helper functions
that define both data and aesthetics and shouldn't inherit behaviour from
the default plot specification, e.g. borders()
.
Moves the text horizontally
Moves the text vertically
Defines the angle in which the text will be placed. *Note
Moves the text vertically an entire contig/sequence.
(e.g. nudge_y = 1
places the text to the contig above)
These labeling functions use ggplot2::geom_text()
under the hood.
Any changes to the aesthetics of the text can be performed in a ggplot2 manner.
# example data
genes <- tibble::tibble(
seq_id = c("A", "A", "A", "B", "B", "C"),
start = c(20, 40, 80, 30, 10, 60),
end = c(30, 70, 85, 40, 15, 90),
feat_id = c("A1", "A2", "A3", "B1", "B2", "C1"),
type = c("CDS", "CDS", "CDS", "CDS", "CDS", "CDS"),
name = c("geneA", "geneB", "geneC", "geneA", "geneC", "geneB"))
seqs <- tibble::tibble(
seq_id = c("A", "B", "C"),
start = c(0,0,0),
end = c(100, 100, 100),
length = c(100, 100, 100))
# basic plot creation
plot <- gggenomes(seqs=seqs, genes=genes) +
geom_bin_label() +
geom_gene()
# geom_..._text
plot + geom_gene_text(aes(label=name))
# geom_..._tag
plot + geom_gene_tag(aes(label=name))
# geom_..._note
plot + geom_gene_note(aes(label=name))
# with horizontal adjustment (`hjust`), vertical adjustment (`vjust`)
plot + geom_gene_text(aes(label=name), vjust = -2, hjust = 1)
# using `nudge_y` and and `angle` adjustment
plot + geom_gene_text(aes(label=name), nudge_y= 1, angle = 10)
# labeling with manual input
plot + geom_gene_text(label = c("This", "is", "an", "example", "test", "test"))