Plot panel of specified embeddings
plotEmbeddings(
embeddings,
groups = NULL,
colors = NULL,
ncol = NULL,
nrow = NULL,
raster = FALSE,
raster.dpi = 300,
panel.size = NULL,
adjust.func = NULL,
title.size = 6,
adj.list = NULL,
subset = NULL,
return.plotlist = FALSE,
...
)
ggplot2 object with the panel of plots
list of two-column matrices with (x, y) coordinates of the embeddings. Each mutrix must have cell names in rownames.
vector of cluster labels, names contain cell names (default=NULL)
vector of numbers, which must be shown with point colors, names contain cell names (default=NULL). This argument is ignored if groups are provided.
number of columns in the panel (default=NULL)
number of rows in the panel (default=NULL)
boolean whether layer with the points be rasterized (default=FALSE). Setting of this argument to TRUE is useful when you need to export a plot with large number of points
dpi of the rasterized plot. (default=300). Ignored if raster == FALSE.
vector with two numbers, which specified (width, height) of the panel in inches (default=NULL). Ignored if raster is FALSE.
function to adjust plots before combining them to single panel (default=NULL). Can be used, for example, to provide color pallette of guides of the plots.
a subset of cells to show (vector of cell names) (default=NULL)
boolean Whether to return a list of ggplot objects instead of a combined plot (default=FALSE)
Arguments passed on to ggrepel::geom_label_repel
data
A data frame. If specified, overrides the default data frame defined at the top level of the plot.
stat
The statistical transformation to use on the data for this layer, as a string.
position
Position adjustment, either as a string, or the result of a call to a position adjustment function.
parse
If TRUE, the labels will be parsed into expressions and displayed as described in ?plotmath
box.padding
Amount of padding around bounding box, as unit or number.
Defaults to 0.25. (Default unit is lines, but other units can be specified
by passing unit(x, "units")
).
label.padding
Amount of padding around label, as unit or number.
Defaults to 0.25. (Default unit is lines, but other units can be specified
by passing unit(x, "units")
).
point.padding
Amount of padding around labeled point, as unit or
number. Defaults to 0. (Default unit is lines, but other units can be
specified by passing unit(x, "units")
).
label.r
Radius of rounded corners, as unit or number. Defaults
to 0.15. (Default unit is lines, but other units can be specified by
passing unit(x, "units")
).
label.size
Size of label border, in mm.
min.segment.length
Skip drawing segments shorter than this, as unit or
number. Defaults to 0.5. (Default unit is lines, but other units can be
specified by passing unit(x, "units")
).
arrow
specification for arrow heads, as created by arrow
force
Force of repulsion between overlapping text labels. Defaults to 1.
force_pull
Force of attraction between a text label and its corresponding data point. Defaults to 1.
max.time
Maximum number of seconds to try to resolve overlaps. Defaults to 0.5.
max.iter
Maximum number of iterations to try to resolve overlaps. Defaults to 10000.
max.overlaps
Exclude text labels that overlap too many things. Defaults to 10.
nudge_x,nudge_y
Horizontal and vertical adjustments to nudge the
starting position of each text label. The units for nudge_x
and
nudge_y
are the same as for the data units on the x-axis and y-axis.
xlim,ylim
Limits for the x and y axes. Text labels will be constrained to these limits. By default, text labels are constrained to the entire plot area.
na.rm
If FALSE
(the default), removes missing values with
a warning. If TRUE
silently removes missing values.
direction
"both", "x", or "y" -- direction in which to adjust position of labels
seed
Random seed passed to set.seed
. Defaults to
NA
, which means that set.seed
will not be called.
verbose
If TRUE
, some diagnostics of the repel algorithm are printed
inherit.aes
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
.