GuitarPlot {Guitar} | R Documentation

## GuitarPlot

### Description

Plot the transcriptomic distribution of genomic features

### Usage

    GuitarPlot(txGTF = NULL,
                txGFF = NULL,
                txGenomeVer = NULL,
                txTxdb = NULL,
                txGuitarTxdb = NULL,
                txGuitarTxdbSaveFile = NA,
                stBedFiles = NULL,
                stGRangeLists = NULL,
                stGroupName = NULL,
                stAmblguity = 5,
                stSampleNum = 10,
                stSampleModle = "Equidistance",
                #stSampleModle = "random",
                txfiveutrMinLength = 100,
                txcdsMinLength = 100,
                txthreeutrMinLength = 100,
                txlongNcrnaMinLength = 100,
                txlncrnaOverlapmrna = FALSE,
                txpromoterLength = 1000,
                txtailLength = 1000,
                txAmblguity = 5,
                txPrimaryOnly = FALSE,
                txTxComponentProp = NULL,
                txMrnaComponentProp = NULL,
                txLncrnaComponentProp = NULL,
                mapFilterTranscript = TRUE,
                headOrtail = TRUE,
                enableCI = TRUE,
                pltTxType =  c("tx","mrna","ncrna"),
                overlapIndex = 1,
                siteLengthIndex = 1,
                adjust = 1,
                CI_ResamplingTime = 1000,
                CI_interval = c(0.025,0.975),
                miscOutFilePrefix = NA)

### Arguments

`txGTF` | GTF file as a source of transcripts.
`txGFF` | txGFF file as a source of transcripts.
`txGenomeVer` | Allows direct provision of genomic assembly numbers, such as "hg19", which is automatically downloaded from makeTxDbFromUCSC.
`txTxdb` | txTxdb file as a source of transcripts.
`txGuitarTxdb` | The processed GuitarCoordinate is used as the source of the transcriptome.
`txGuitarTxdbSaveFile` | Return the generated GuitarTxdb to a file.
`stBedFiles` | BED file as a source of Site.
`stGRangeLists` | GRange data structure as a source of Site.
`stGroupName` | Group names of Sites.
`stAmblguity` | Maximum overlap between sites. Default: 5.
`stSampleNum` | The number of bases sampled at each Site. Default: 3.
`stSampleModle` | sampling "Equidistance",sampling "random". Default:"Equidistance".
`txfiveutrMinLength` | 5'UTR length. Default: 100.
`txcdsMinLength` | CDS length. Default: 100.
`txthreeutrMinLength` | 3'UTR length. Default: 100.
`txlongNcrnaMinLength` | lncrna length. Default: 100.
`txlncrnaOverlapmrna` | Whether to allow lncRNA to overlap with mRNA. Default: FALSE.
`txpromoterLength` | promoter length. Default: 1000.
`txtailLength` | tail length. Default: 1000.
`txAmblguity` | Maximum overlap between Tx. Default: 5.
`txPrimaryOnly` | Whether to use only the main Tx. Default: FALSE.
`txTxComponentProp` | If it is "NULL", the proportion of the promoter/tx/tail of TX is automatically calculated according to the transcriptome, otherwise, the user specifies the proportion of each part.
`txMrnaComponentProp` | If it is "NULL", the proportion of promoter/5'UTR/CDS/3'UTR/tail of mrna is automatically calculated according to the transcriptome. Otherwise, the user specifies the proportion of each part.
`txLncrnaComponentProp` | If it is "NULL", the proportion of promoter/tx/tail of lncRNA is automatically calculated according to the transcriptome, otherwise the user specifies the proportion of each part.
`mapFilterTranscript` | Whether to filter the length of transcripts equal the original site. Default: TRUE.
`headOrtail` | Whether to retain promoter and tail. Default: TRUE.
`enableCI` | Whether to add a CI curve. Default: TRUE.
`pltTxType` | Which transcript is to be drawn on. If there is no such transcript in the genome, it cannot be drawn even if specified. Default: c("tx","mrna","ncrna").
`overlapIndex` | Index of site overlapping times. Default: 1.
`siteLengthIndex` | Index of site length. Default: 1.
`CI_ResamplingTime` | Resampling times in density drawing mode. Default: 1000.
`CI_interval` | Upper and lower limits of the confidence interval. Default : c(0.025,0.975).
`adjust` | Curve's smooth level. Default: 1.
`miscOutFilePrefix` | Save as a PDF name prefix, If the prefix is not specified, we will default the PDF name to "Guitar-type-test.PDF".

### Details

This function plots the transcriptomic distribution of genomic features. It is designed for a fast usage of the Guitar package, When you need to specify a parameter, you need to define the function when the package is called.

### 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.

### Author(s)

Xiao Du <xiao.du@cumt.edu.cn>

### Examples

    # read transcript information
    txdb_file <- system.file("extdata", "mm10_toy.sqlite", package="Guitar")
    txdb <- loadDb(txdb_file)
    # read genomic features
    stGRangelist<-list()
    stBedFiles <- list(system.file("extdata", "m6A_mm10_exomePeak_1000peaks_bed12.bed", package="Guitar"))
    for (i in 1:length(stBedFiles)) {
      stGRangelist[[i]] <-  blocks(import(stBedFiles[[i]]))
    }
    #plot
    GuitarPlot(txTxdb = txdb,
                    stGRangeLists = stGRangelist,
                    stGroupName = c("Group1"))

[Package Guitar version 2.8.0 Index]