plotGene: Visual representation of gene expression.
In wjawaid/bglab: Berthold Gottgens lab scRNA seq

Description Usage Arguments Details Value Author(s)

Plots dimensionality reduced object with points coloured by level of gene expression.

plotGene(scd, gene, useDims = 1:2, reduceMethod = c("pca", "diffMap",
  "tsne", "isomap"), lcol = "grey", hcol = "red", use.ggPlot = FALSE,
  main = gene, pch = 20, includeHidden = FALSE, bringToFront = TRUE,
  project2D = NULL, opacity = NULL, legPos = "topright",
  empty.channel = c(0.2, 0.2, 0.2, 0.5), adjust = 0, minVal = NULL,
  maxVal = NULL, legend = FALSE, multigene = FALSE, useMeta = FALSE,
  bgCol = "black", leg.text.col = "white", leg.inset = 0,
  plt.mar = rep(0, 4), channelOrder = 1:3, ...)

`scd`	single cell dataset object
`gene`	Gene to be visualised.
`useDims`	dimensions to be used
`reduceMethod`	The dimensionality reduction technique to be used
`lcol`	Colour to be taken for low values. Default is "grey".
`hcol`	Colour to be taken by high values. Default is "red".
`use.ggPlot`	Plot using ggPlots or native R graphics.
`main`	Plot title. Defaults to gene name.
`pch`	Point caharcter. Default is 16.
`includeHidden`	Default FALSE, will only include highly variable genes.
`bringToFront`	Bring high values to fore.
`project2D`	Default NULL. Projects 3D graph into 2D by the given transformation matrix. This matrix must have been produced using `getMVP` on an open rgl device.
`opacity`	Default NULL. Set opacity.
`legPos`	Default "topright". Position of legend
`empty.channel`	Default (0.2,0.2,0.2). Sets the zero state of cell not expressing anything
`adjust`	Default (0,0,0). Adjustment for red, green and blue channel, respectively.
`minVal`	Default NULL. Set the maximum and minimum color values manually.
`maxVal`	Default NULL. Set the maximum and minimum color values manually.
`legend`	Default FALSE. Plot legend or not.
`multigene`	Default FALSE. For internal use indicating function is being called from the multiGene() function.
`useMeta`	Default FALSE. To use information from the meta data.
`bgCol`	Default black. Background colour.
`leg.text.col`	Default white. Legend text colour.
`leg.inset`	Default 0. Legend inset.
`plt.mar`	Default rep(0,4). Plot margins
`channelOrder`	Default 1:3 indicating red, green, blue.
`...`	Additional parameters to pass to plot