heatmapfCCAC {fCCAC} | R Documentation

## Heatmap of F values obtained by Canonical Correlation Analysis

### Description

Heatmap of F values obtained by Canonical Correlation Analysis. This function can only be used if all pairwise comparisons were computed previously with the function 'fccac', i.e., using "tf=c()".

### Usage

      heatmapfCCAC(fc)

### Arguments

`fc` | Output of the function 'fccac'.

### Value

Plots a Heatmap of F values using the package 'ComplexHeatmap'.

### Author(s)

Pedro Madrigal, pmadrigal@ebi.ac.uk

### References

Madrigal P (2016) fCCAC: functional canonical correlation analysis to evaluate covariance between nucleic acid sequencing datasets. Bioinformatics: http://doi.org/10.1093/bioinformatics/btw724.

### See Also

`fccac`

### Examples

      ## hg19. chr21:40000000-48129895 H3K4me3 data from Bertero et al. (2015)
      if (.Platform$OS.type == "unix") {

        owd <- setwd(tempdir())

        bigwig1 <- "chr21_H3K4me3_1.bw"
        bigwig2 <- "chr21_H3K4me3_2.bw"
        bigwig3 <- "chr21_H3K4me3_3.bw"
        peakFile <- "chr21_merged_ACT_K4.bed"
        labels <- c( "H3K4me3", "H3K4me3","H3K4me3" )

        r1 <- system.file("extdata", bigwig1,  package="fCCAC",mustWork = TRUE)
        r2 <- system.file("extdata", bigwig2,  package="fCCAC",mustWork = TRUE)
        r3 <- system.file("extdata", bigwig3,  package="fCCAC",mustWork = TRUE)
        r4 <- system.file("extdata", peakFile, package="fCCAC",mustWork = TRUE)
        ti <- "H3K4me3 peaks"

        fc <- fccac(bar=NULL, main=ti, peaks=r4, bigwigs=c(r1,r2,r3), labels=labels, splines=15, nbins=100, ncan=15)

        head(fc)

        heatmapfCCAC(fc)

        setwd(owd)

      }

[Package fCCAC version 1.20.0 Index]