Guitar (version 1.10.0)

GuitarPlot: GuitarPlot

Description

Plot the transcriptomic distribution of genomic features

Usage

GuitarPlot(gfeatures, GuitarCoordsFromTxDb = NA,  txdb = NA, genome = NA,  noBins = 10, saveToPDFprefix = NA,  returnCount = FALSE, includeNeighborDNA = FALSE, maximalFeatureAmbiguity=5, rescaleComponent=TRUE, fill=FALSE)

Arguments

gfeatures

genomic features, which can be GRanges, GRangesList, GAlignment.

GuitarCoordsFromTxDb

Guitar coordiantes generated from makeGuitarCoordsFromTxDb object

txdb

If GuitarCoordsFromTxDb is not provided, you may optionally provide a TranscriptDb object, and the Guitar coordiante will be generated accordingly from it.

genome

If neither GuitarCoordsFromTxDb nortxdb is not provided, you may optionally provide genome assembly number, gene annotation will be automatically downloaded from UCSC, and the Guitar coordiante will be generated accordingly from it.

noBins

The resolution of the analysis. Default: 100

saveToPDFprefix

Whether the figure generated should be saved into a PDF file.

returnCount

Whether the count information should be returned. This information is from countOverlaps between the provided gfeatures and Guitar coordiantes. It is not recommended to use this information.

includeNeighborDNA

Whether neighborhood DNA regions should be included in the GuitarPlot.

maximalFeatureAmbiguity

Features that overlap with more than this number of transcripts will not be used in the analysis. If a genomic feature overlaps with multiple transcripts but the number doesn't exceed this threshold, its weight will be evenly divided. Default: 5

rescaleComponent

Whether the actual length of different components should be reflected in the generated figure. 5'UTR is usually much shorter than other components, so if this option is turned on, 5'UTR can be difficult to be observed; however, this difficulty is resulted from its short width. Default: TRUE.

fill

Whether calculate the relative location-standardized density or not. If set "TRUE", the density of tracks will be standardized with respect to each location. Default: FALSE

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.

Details

This function plots the transcriptomic distribution of genomic features. It is designed for a fast usage of the Guitar package without the needs to go into the details.

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]
feature_hg19 <- list(m6A_Bcell_1, m6A_Bcell_2, m6A_Bcell_3) 
names(feature_hg19) <- c("m6A_1","m6A_2","m6A_3")

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


# Plot
GuitarPlot(feature_hg19, 
           GuitarCoordsFromTxDb = gc_txdb)