| combinedGuitarPlot {Guitar} | R Documentation |
combine multiple GuitarPlots, especially when they are from different species and cannot directly handled with GuitarPlot function together.
combinedGuitarPlot(ct, comLength = c(0.136,0.459, 0.405))
ct |
Count of overlapping features, which is can be the output from GuitarPlot function. See example. |
comLength |
a vector of 3 elements,indicating the length of 5'UTR, CDS and 3'UTR in the figure. Default: c(0.136,0.459, 0.405), which is counted from the default setting of hg19 UCSC gene annotation. |
combine multiple GuitarPlots, especially when they are from different species.
A figure showing the transcriptomic distribution of the genomic features will be generated. Post-editing with Adobe Illustrator or other graphic software is recommended.
# 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]
m6A_Bcell_4 <- m6A_Bcell[201:900]
# Make Guitar coordiantes
txdb_file <- system.file("extdata", "hg19_toy.sqlite",
package="Guitar")
txdb <- loadDb(txdb_file)
gc_txdb <- makeGuitarCoordsFromTxDb(txdb,noBins =10)
# Guitar plot 1
feature1_hg19 <- list(m6A_Bcell_1, m6A_Bcell_2)
names(feature1_hg19) <- c("m6A_1","m6A_2")
ct1 <- GuitarPlot(feature1_hg19, returnCount = TRUE,
GuitarCoordsFromTxDb = gc_txdb)
# Guitar plot 2
feature2_hg19 <- list(m6A_Bcell_3, m6A_Bcell_4)
names(feature2_hg19) <- c("m6A_3","m6A_4")
ct2 <- GuitarPlot(feature2_hg19, returnCount = TRUE,
GuitarCoordsFromTxDb = gc_txdb)
# combine two Gutiar Plot
ct <- rbind(ct1,ct2)
combinedGuitarPlot(ct)