plotCNA {MesKit} | R Documentation

## plotCNA

### Description

plotCNA

### Usage

    plotCNA(
      seg,
      patient.id = NULL,
      sampleOrder = NULL,
      chrSilent = NULL,
      refBuild = "hg19",
      sample.text.size = 11,
      chrom.text.size = 3,
      legend.text.size = 9,
      legend.title.size = 11,
      annot.text.size = 3,
      sample.bar.height = 0.5,
      chrom.bar.height = 0.5,
      showRownames = TRUE,
      removeEmptyChr = TRUE,
      showCytoband = FALSE,
      showGene = FALSE,
      use.tumorSampleLabel = FALSE
    )

### Arguments

`seg` | Object generated by `readSegment` function.
`patient.id` | Select the specific patients. Default NULL, all patients are included.
`sampleOrder` | A named list which contains the sample order used in plotting the final profile. Default NULL.
`chrSilent` | Chromosomes excluded in the analysis. e.g, 1, 2, 3. Default NULL.
`refBuild` | Human reference genome versions of hg18, hg19 or hg38 by UCSC. Default "hg19".
`sample.text.size` | Fontsize of sample name. Default 11.
`chrom.text.size` | Fontsize of chromosome text. Default 3.
`legend.text.size` | Fontsize of legend text. Default 9.
`legend.title.size` | Fontsize of legend title. Default 11.
`annot.text.size` | Fontsize of cytoband or gene symbols. Default 3.
`sample.bar.height` | Bar height of each sample. Default 0.5.
`chrom.bar.height` | Bar height of each chromosome. Default 0.5.
`showRownames` | Logical (Default: TRUE). Show sample names of rows.
`removeEmptyChr` | Remove empty chromosomes that do not exist in all samples. Default TRUE.
`showCytoband` | Logical (Default: FALSE). Show cytobands on the plot. Only when the seg object is created with GISTIC results, this parameter can be TRUE.
`showGene` | Logical (Default: FALSE). Show gene symbols on the plot. Only when the seg object is created with txdb, this parameter can be TRUE.
`use.tumorSampleLabel` | Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' with 'Tumor_Sample_Label'.

### Value

a heatmap plot of CNA profile

### Examples

    segFile <- system.file("extdata", "CRC_HZ.seg.txt", package = "MesKit")
    seg <- readSegment(segFile = segFile)
    plotCNA(seg)

    ## showCytoband
    gisticAmpGenesFile <- system.file("extdata", "COREAD_amp_genes.conf_99.txt", package = "MesKit")
    gisticDelGenesFile <- system.file("extdata", "COREAD_del_genes.conf_99.txt", package = "MesKit")
    gisticAllLesionsFile <- system.file("extdata", "COREAD_all_lesions.conf_99.txt", package = "MesKit")
    seg <- readSegment(segFile = segFile,
                       gisticAmpGenesFile = gisticAmpGenesFile,
                        gisticDelGenesFile = gisticDelGenesFile,
                       gisticAllLesionsFile = gisticAllLesionsFile)
    plotCNA(seg, showCytoband = TRUE)

[Package MesKit version 1.4.0 Index]