GuitarPlot: GuitarPlot

Description Usage Arguments Details Value Author(s) Examples

View source: R/GuitarPlot.R

Description

Plot the transcriptomic distribution of genomic features

Usage

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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

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# 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"))

Guitar documentation built on Nov. 8, 2020, 5:15 p.m.