ggGeneOnTSNE: Plot gene expression on tSNE map
In Japrin/sscVis: simpler single cell RNAseq data Visualization

ggGeneOnTSNE

R Documentation

Plot gene expression on tSNE map

Description

Plot gene expression on tSNE map

Usage

ggGeneOnTSNE(
  Y,
  dat.map,
  gene.to.show,
  out.prefix = NULL,
  p.ncol = 3,
  theme.use = theme_bw,
  xlim = NULL,
  ylim = NULL,
  size = NULL,
  pt.alpha = 0.5,
  pt.order = "value",
  clamp = NULL,
  palette.name = "YlOrRd",
  verbose = F,
  fun.extra = NULL,
  width = 9,
  height = 8,
  scales = "fixed",
  my.ggPoint = geom_point,
  par.geom_point = list(),
  par.legend = list(),
  splitBy = NULL
)

Arguments

`Y`	matrix or data.frame; Gene expression data, rownames shoud be gene id, colnames should be sample id
`dat.map`	data.frame; tSNE map, must be two columns data.frame and rownames should be sample id
`gene.to.show`	character; gene id to be showd on the tSNE map
`out.prefix`	character; output prefix (default: NULL)
`p.ncol`	integer; number of columns in the plot's layout (default: 3)
`theme.use`	function; which theme to use (default: theme_bw)
`xlim`	integer or NULL; only draw points lie in the ragne specified by xlim and ylim (default NULL)
`ylim`	integer or NULL; only draw points lie in the ragne specified by xlim and ylim (default NULL)
`size`	double; points' size. If NULL, infer from number of points (default NULL)
`pt.alpha`	numeric; alpha of the points (default: 0.5)
`pt.order`	character; (default: "value")
`clamp`	integer vector; expression values will be clamped to the range defined by this parameter, such as c(0,15). (default: NULL )
`palette.name`	character; which palette to use, such as "RdBu","RdYlBu" (default: NULL)
`verbose`	logical; (default: FALSE)
`fun.extra`	function; (default: NULL)
`width`	numeric; width of the plot (default: 9)
`height`	numeric; height of the plot (default: 8)
`scales`	character; whether use the same scale across genes. one of "fixed" or "free" (default: "fixed")
`my.ggPoint`	function; used to plot scatter plot, such as geom_point, geom_point_rast, geom_scattermore, geom_scattermost (default: geom_point)
`par.geom_point`	list; extra parameters for geom_point/geom_point_rast; (default: list())
`par.legend`	list; lengend parameters, used to overwrite the default setting; (default: list())
`splitBy`	character; split by (default: NULL)

Details

For genes contained in both 'Y' and 'gene.to.show', show their expression on the tSNE map provided as 'dat.map'. One point in the map represent a cell; cells with higher expression also have darker color.