plotFeatureSingle: plotFeatureSingle Allow the object can be a matrix of...
In beyondpie/pureRUtils: Commonly used R functions with pure R codes

plotFeatureSingle

R Documentation

plotFeatureSingle Allow the object can be a matrix of umap/tsne or a snap

Description

plotFeatureSingle Allow the object can be a matrix of umap/tsne or a snap

Usage

plotFeatureSingle(
  snap = NULL,
  featureValue,
  embedmat = NULL,
  method = c("tsne", "umap"),
  downSample = 10000,
  pdfile = NULL,
  pdfWidth = 7,
  pdfHeight = 7,
  quantiles = c(0.01, 0.99),
  pal = viridis::viridis(n = 256),
  colorTitle = "gene score",
  pointSize = 0.1,
  labelSize = 5,
  baseSize = 12,
  legendSize = 8,
  discrete = FALSE,
  labelMeans = FALSE,
  quantile.na.rm = TRUE,
  showLegend = FALSE,
  ...
)

Arguments

`snap`	A snap object, default is NULL
`featureValue`	Feature enrichment value for each cell. Value will be normalized betweeen 0 and 1.
`embedmat`	a matrix of umap or tsne, default is NULL
`method`	Visulization method c("tsne", "umap").
`downSample`	Downsample the original cells to down.sample cells to ovoid large dataset 10,000.
`pdfile`	pdf file name to save the plot NULL.
`pdfWidth`	Width of the graphics region in inches 7.
`pdfHeight`	Height of the graphics region in inches 7.
`quantiles`	Feature value outside this range will be removed c(0.01, 0.99)
`pal`	colors for ploting continuous numbers, default viridis::viridis(n=256)
`colorTitle`	legend title, default is "gene score"
`pointSize`	numeric, default is 0.1
`labelSize`	integer default is 5
`baseSize`	integer default is 12
`legendSize`	integer default is 8
`discrete`	bool is featureValue discrete, default is FALSE
`labelMeans`	bool if label the position of means, default is FALSE This is usually needed when discrete is TRUE
`quantile.na.rm`	bool if remove NA values when using quantile function default is TRUE, this is usually used for continuous feature values.
`showLegend`	bool default is FALSE
`...`	Arguments passed to ggPoint method