plotSamples: Plot panel of specified embeddings, extracting them from...

Description Usage Arguments Value

View source: R/plot.R

Description

Plot panel of specified embeddings, extracting them from pagoda2 objects

Usage

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plotSamples(
  samples,
  groups = NULL,
  colors = NULL,
  gene = NULL,
  embedding.type = NULL,
  ...
)

Arguments

samples

list of pagoda2 or Seurat objects

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.

gene

gene name (default=NULL). If this parameter is provided, points are colored by expression of this gene.

embedding.type

type of embedding (default=NULL). If embedding.type is NULL, this defaults to 'tSNE'. If a matrix is passed, it is interpreted as an actual embedding (then first two columns are interpreted as x/y coordinates, row names must be cell names).

...

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

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.

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

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.

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 with the panel of plots


conos documentation built on Feb. 23, 2021, 9:06 a.m.