make.gene.model {iCellR}

Make a gene model for clustering

Description

This function takes an object of class iCellR and provides a gene list for clustering based on the parameters set in the model.

Usage

make.gene.model(
  x = NULL,
  dispersion.limit = 1.5,
  base.mean.rank = 500,
  gene.num.max = 2000,
  non.sig.col = "darkgray",
  right.sig.col = "chartreuse3",
  left.sig.col = "cadetblue3",
  disp.line.col = "black",
  rank.line.col = "red",
  my.out.put = "data",
  cell.size = 1.75,
  cell.transparency = 0.5,
  no.mito.model = TRUE,
  no.cell.cycle = TRUE,
  mark.mito = TRUE,
  interactive = TRUE,
  out.name = "plot"
)

Arguments

x

An object of class iCellR.

dispersion.limit

A number for taking the genes that have dispersion above this number, default = 1.5.

base.mean.rank

A number taking the top genes ranked by base mean, default = 500.

gene.num.max

Maximum number of genes , default = 2000.

non.sig.col

Color for the genes not used for the model, default = "darkgray".

right.sig.col

Color for the genes above the dispersion limit, default = "chartreuse3".

left.sig.col

Color for the genes above the rank limit, default = "cadetblue3".

disp.line.col

Color of the line for dispersion limit, default = "black".

rank.line.col

Color of the line for rank limit, default = "red".

my.out.put

Chose from "data" or "plot", default = "data".

cell.size

A number for the size of the points in the plot, default = 1.75.

cell.transparency

Color transparency for the points in the plot, default = 0.5.

no.mito.model

If set to TRUE, mitochondrial genes would be excluded from the gene list made for clustering, default = TRUE.

no.cell.cycle

If TRUE the cell cycle genes will be removed (s.phase and g2m.phase), default = TRUE.

mark.mito

Mark mitochondrial genes in the plot, default = TRUE.

interactive

If set to TRUE an interactive HTML file will be created, default = TRUE.

out.name

If "interactive" is set to TRUE, the out put name for HTML, default = "plot".

Value

An object of class iCellR.