RepViz {RepViz} | R Documentation |
Plot a genomic region
RepViz(region, genome = c("hg19", "hg38", "mm10"), BAM = NULL, BED = NULL, avgTrack = TRUE, geneTrack = TRUE, max = NULL, verbose = TRUE, cex = 1)
region |
a GRange object with chr, start, end |
genome |
a character vector 'hg19','hg38' or 'mm10' |
BAM |
a path to the BAM related csv input file |
BED |
a path to the BED related csv input file |
avgTrack |
a logical indicating if the average track should be included or not |
geneTrack |
a logical indicating if the gene track should be included or not |
max |
a numerical vector containing the yaxis maximum value of each BAM track |
verbose |
a logical indicating whether the progress of the plotting is shown |
cex |
number indicating the amount by which plotting text and symbols should be scaled relative to the default. |
col |
vector of character user can set color of the different BED tracks. |
displays the region specified by the user
region <- GRanges('chr12:110938000-110940000') setwd(tempdir()) #Copying the files to the user working directory file.copy(from = list.files(system.file('extdata', package = 'RepViz'), full.names = TRUE), to = tempdir()) #Generate the visualization of the given region RepViz::RepViz(region = region, genome = 'hg19', BAM = 'BAM_input.csv', BED = 'BED_input.csv', avgTrack = TRUE, geneTrack = TRUE)