GuitarPlot {Guitar} | R Documentation |
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"))