combinedGuitarPlot {Guitar} | R Documentation

## combinedGuitarPlot

### Description

combine multiple GuitarPlots, especially when they are from different species and cannot directly handled with GuitarPlot function together.

### Usage

    combinedGuitarPlot(ct, comLength = c(0.136,0.459, 0.405))

### Arguments

`ct` | Count of overlapping features, which is can be the output from GuitarPlot function. See example.
`comLength` | a vector of 3 elements,indicating the length of 5'UTR, CDS and 3'UTR in the figure. Default: c(0.136,0.459, 0.405), which is counted from the default setting of hg19 UCSC gene annotation.

### Details

combine multiple GuitarPlots, especially when they are from different species.

### Value

A figure showing the transcriptomic distribution of the genomic features will be generated. Post-editing with Adobe Illustrator or other graphic software is recommended.

### Examples

    # read genomic features
    narrowPeak <- system.file(
      "extdata", "m6A_hg19_1000peaks_macs2.narrowPeak",
      package="Guitar")

    # bam imported as GAlignments
    m6A_Bcell <- narrowPeaktoGRanges(narrowPeak)

    # generate a list of genomic features
    m6A_Bcell_1 <- m6A_Bcell[1:300]
    m6A_Bcell_2 <- m6A_Bcell[301:600]
    m6A_Bcell_3 <- m6A_Bcell[601:900]
    m6A_Bcell_4 <- m6A_Bcell[201:900]

    # Make Guitar coordiantes
    txdb_file <- system.file("extdata", "hg19_toy.sqlite",
                             package="Guitar")
    txdb <- loadDb(txdb_file)
    gc_txdb <- makeGuitarCoordsFromTxDb(txdb,noBins =10)

    # Guitar plot 1
    feature1_hg19 <- list(m6A_Bcell_1, m6A_Bcell_2)
    names(feature1_hg19) <- c("m6A_1","m6A_2")
    ct1 <- GuitarPlot(feature1_hg19, returnCount = TRUE,
               GuitarCoordsFromTxDb = gc_txdb)

    # Guitar plot 2
    feature2_hg19 <- list(m6A_Bcell_3, m6A_Bcell_4)
    names(feature2_hg19) <- c("m6A_3","m6A_4")
    ct2 <- GuitarPlot(feature2_hg19, returnCount = TRUE,
               GuitarCoordsFromTxDb = gc_txdb)

    # combine two Gutiar Plot
    ct <- rbind(ct1,ct2)
    combinedGuitarPlot(ct)

[Package Guitar version 1.18.0 Index]