geom_coverage | R Documentation |
Visualize data that varies along sequences as ribbons, lines, lineranges, etc.
geom_coverage(
mapping = NULL,
data = feats(),
stat = "coverage",
geom = "ribbon",
position = "identity",
na.rm = FALSE,
show.legend = NA,
inherit.aes = TRUE,
offset = 0,
height = 0.2,
max = base::max,
...
)
geom_wiggle(
mapping = NULL,
data = feats(),
stat = "wiggle",
geom = "ribbon",
position = "identity",
na.rm = FALSE,
show.legend = NA,
inherit.aes = TRUE,
offset = 0,
height = 0.8,
bounds = Hmisc::smedian.hilow,
...
)
mapping |
Set of aesthetic mappings created by |
data |
The data to be displayed in this layer. There are three options: If A A |
stat |
The statistical transformation to use on the data for this layer.
When using a
|
geom |
The geometric object to use to display the data for this layer.
When using a
|
position |
A position adjustment to use on the data for this layer. This
can be used in various ways, including to prevent overplotting and
improving the display. The
|
na.rm |
If |
show.legend |
logical. Should this layer be included in the legends?
|
inherit.aes |
If |
offset |
distance between seq center and wiggle mid/start. |
height |
distance in plot between lowest and highest point of the wiggle data. |
max |
geom_coverage uses the function base::max by default, which plots data in positive direction. (base::min Can also be called here when the input data ) |
... |
Other arguments passed on to
|
bounds |
geom_wiggle uses mid, low and high boundary values for plotting wiggle data. Can be both a function or a vector returning those three values. Defaults to Hmisc::smedian.hilow. |
Geom_wiggle plots the wiggle data in both directions around the median. Geom_coverage plots the data only in positive direction. Both functions use data from the feats' track.
A ggplot2 layer with coverage information.
geom_wiggle()
and geom_coverage()
understand aesthetics depending on the
chosen underlying ggplot geom, by default ggplot2::geom_ribbon()
. Other
options that play well are for example ggplot2::geom_line()
,
ggplot2::geom_linerange()
, ggplot2::geom_point()
. The only required
aesthetic is:
z
# Plotting data with geom_coverage with increased height.
gggenomes(seqs = emale_seqs, feats = emale_gc) +
geom_coverage(aes(z = score), height = 0.5) +
geom_seq()
# In opposite direction by calling base::min and taking the negative values of "score"
gggenomes(seqs = emale_seqs, feats = emale_gc) +
geom_coverage(aes(z = -score), max = base::min, height = 0.5) +
geom_seq()
# GC-content plotted as points with variable color in geom_coverage
gggenomes(seqs = emale_seqs, feats = emale_gc) +
geom_coverage(aes(z = score, color = score), height = 0.5, geom = "point") +
geom_seq()
# Plot varying GC-content along sequences as ribbon
gggenomes(seqs = emale_seqs, feats = emale_gc) +
geom_wiggle(aes(z = score)) +
geom_seq()
# customize color and position
gggenomes(genes = emale_genes, seqs = emale_seqs, feats = emale_gc) +
geom_wiggle(aes(z = score), fill = "lavenderblush3", offset = -.3, height = .5) +
geom_seq() + geom_gene()
# GC-content as line and with variable color
gggenomes(seqs = emale_seqs, feats = emale_gc) +
geom_wiggle(aes(z = score, color = score), geom = "line", bounds = c(.5, 0, 1)) +
geom_seq() +
scale_colour_viridis_b(option = "A")
# or as lineranges
gggenomes(seqs = emale_seqs, feats = emale_gc) +
geom_wiggle(aes(z = score, color = score), geom = "linerange") +
geom_seq() +
scale_colour_viridis_b(option = "A")
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