sc_marker2color {sincell} | R Documentation

## 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)

[Package sincell version 1.22.0 Index]