sincell (version 1.4.2)

sc_marker2color: Palette of colors from the expression values of a marker gene

Description

Function that transforms the expression values of a marker gene into a vector of colors that can be used as a color code for the intensity of expression. First, the function extracts the vector of values form the expression matrix row in SincellObject[["expressionmatrix"]] whose name equals the indicated marker. Then those values are transformed into a color scale in which the minimum value is assigned the color "minimum" and the maximum value the color "maximum". If relative.to.marker=TRUE, the minimum and maximum values are taken from the expression values of the marker. If relative.to.marker=FALSE, the minimum and maximum values are taken from the expression values of the entire expression matrix.

Usage

sc_marker2color(SincellObject, marker, color.minimum="green", 
  color.maximum="red", relative.to.marker=TRUE)

Arguments

SincellObject

A SincellObject named list as created by function sc_InitializingSincellObject with a named member "expressionmatrix" containing a numeric matrix that represents a gene expression matrix gathering the expression levels of each single-cell in the experiment (displayed by columns) for each detected gene (displayed by rows).

marker

Name of the gene marker. It should correspond to a row name in the expression matrix in SincellObject[["expressionmatrix"]]

color.minimum

Color that will be assigned to the minimum expression value

color.maximum

Color that will be assigned to the maximum expression value

relative.to.marker

Logic indicating whether the minimum and maximum values are taken from the expression values of the marker (relative.to.marker=TRUE) or from the entire expression matrix (relative.to.marker=FALSE)

Value

• The function returns an array of colors in hexadecimal format

Examples

## Generate some random data
Data <- matrix(abs(rnorm(3000, sd=2)),ncol=10,nrow=30)

## Initializing SincellObject named list
mySincellObject <- sc_InitializingSincellObject(Data)

## Adding gene names to expression matrix
rownames(mySincellObject[["expressionmatrix"]]) <- 1:30

## Getting the color vector coding for the expression values of a marker gene
mymarkerColorCodeA<-sc_marker2color(mySincellObject, marker="3", 
  color.minimum="green", color.maximum="red", relative.to.marker=TRUE)
mymarkerColorCodeB<-sc_marker2color(mySincellObject, marker="5", 
  color.minimum="yellow", color.maximum="blue", relative.to.marker=FALSE)