embeddingColorsPlot {sccore}

Set colors for embedding plot. Used primarily in embeddingPlot().

Description

Set colors for embedding plot. Used primarily in embeddingPlot().

Usage

embeddingColorsPlot(
  plot.df,
  colors,
  groups = NULL,
  geom_point_w = ggplot2::geom_point,
  gradient.range.quantile = 1,
  color.range = "symmetric",
  legend.title = NULL,
  palette = NULL,
  plot.na = TRUE
)

Arguments

plot.df

data.frame for plotting. In embeddingPlot(), this is a tibble from tibble::rownames_to_column().

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.

groups

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

geom_point_w

function to work with geom_point layer from ggplot2 (default=ggplot2::geom_point)

gradient.range.quantile

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

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.

legend.title

legend title (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)

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

Value

ggplot2 object