embeddingPlot {sccore}

Plot embedding with provided labels / colors using ggplot2

Description

Plot embedding with provided labels / colors using ggplot2

Usage

embeddingPlot(
  embedding,
  groups = NULL,
  colors = NULL,
  subgroups = NULL,
  plot.na = is.null(subgroups),
  min.cluster.size = 0,
  mark.groups = TRUE,
  show.legend = FALSE,
  alpha = 0.4,
  size = 0.8,
  title = NULL,
  plot.theme = NULL,
  palette = NULL,
  color.range = "symmetric",
  font.size = c(3, 7),
  show.ticks = FALSE,
  show.labels = FALSE,
  legend.position = NULL,
  legend.title = NULL,
  gradient.range.quantile = 1,
  raster = FALSE,
  raster.dpi = 300,
  shuffle.colors = FALSE,
  keep.limits = !is.null(subgroups),
  ...
)

Arguments

embedding

two-column matrix with x and y coordinates of the embedding, rownames contain cell names and are used to match coordinates with groups or colors

groups

vector of cluster labels, names contain cell names (default=NULL)

colors

vector of numbers, which must be shown with point colors, names contain cell names (default=NULL). This argument is ignored if groups are provided.

subgroups

subset of 'groups', selecting the cells for plot (default=NULL). Ignored if 'groups' is NULL

plot.na

boolean/numeric Whether to plot points, for which groups / colors are missed (default=is.null(subgroups), i.e. FALSE). If plot.na passed a numeric value below 0, the NA symbols are plotted below the cells. Otherwise if values >=0, they’re plotted above the cells. Note that this argument is FALSE if 'subgroups' is NULL

min.cluster.size

labels for all groups with number of cells fewer than this parameter are considered as missed (default=0). This argument is ignored if groups aren't provided

mark.groups

plot cluster labels above points (default=TRUE)

show.legend

show legend (default=FALSE)

alpha

opacity level [0, 1] (default=0.4)

size

point size (default=0.8)

title

plot title (default=NULL)

plot.theme

theme for the plot (default=NULL)

palette

vector or list or function (default=NULL). Accepts number of colors and return list of colors (i.e. see 'colorRampPalette') (default=NULL)

color.range

controls range, in which colors are estimated (default="symmetric"). Pass "all" to estimate range based on all values of "colors", pass "data" to estimate it only based on colors, presented in the embedding. Alternatively you can pass vector of length 2 with (min, max) values.

font.size

font size for cluster labels (default=c(3, 7)). It can either be single number for constant font size or pair (min, max) for font size depending on cluster size

show.ticks

show ticks and tick labels (default=FALSE)

show.labels

show labels (default=FALSE)

legend.position

vector with (x, y) positions of the legend (default=NULL)

legend.title

legend title (default=NULL)

gradient.range.quantile

Winsorization quantile for the numeric colors and gene gradient (default=1)

raster

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

raster.dpi

dpi of the rasterized plot. (default=300). Ignored if raster == FALSE.

shuffle.colors

shuffle colors (default=FALSE)

keep.limits

Keep axis limits from original plot (default=!is.null(subgroups)). Useful when plotting subgroups, only meaningful it plot.na=FALSE

...

Arguments passed on to ggrepel::geom_label_repel

mapping

Set of aesthetic mappings created by aes or aes_. If specified and inherit.aes = TRUE (the default), is combined with the default mapping at the top level of the plot. You only need to supply mapping if there isn't a mapping defined for the plot.

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.

Value

ggplot2 object

Examples

library(sccore)
embeddingPlot(umapEmbedding, show.ticks=TRUE, show.labels=TRUE, title="UMAP embedding")