GuitarPlot: GuitarPlot
In Guitar: Guitar

Description Usage Arguments Details Value Author(s) Examples

View source: R/GuitarPlot.R

Plot the transcriptomic distribution of genomic features

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)

`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".

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.

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

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

# 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"))