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

In sincell: R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data

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)

Example output

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

sincell documentation built on Nov. 8, 2020, 5:58 p.m.