drawingKaryo: Draw the karyogram plot.

In RIPAT: Retroviral Integration Pattern Analysis Tool (RIPAT)

Description

Draw a karyogram plot and show integration site.

Usage

drawingKaryo(hits, feature, organism = 'GRCh37',
             includeUndecided = FALSE, outPath = getwd(), 
             outFileName = paste0('RIPAT', round(unclass(Sys.time()))))

Arguments

hits	a GR object. This object made from makeInputObj function.
feature	a GR object. This object made from annotation function.
organism	a character vector. This function serves 2 versions of organisms such as GRCh37, GRCh38 (Human). Default is 'GRCh37'.
includeUndecided	TRUE or FALSE. If user want to use undecided hits in analysis, enter TRUE. Default is FALSE.
outPath	a string vector. Type path to save a plot.
outFileName	a character vector. This value used when saving the idegoram image file.

Value

Return the ideogram plot and object.

Examples

data(blast_obj)
data(blast_gene)
drawingKaryo(hits = blast_obj, feature = blast_gene$Gene_data, outFileName = 'blast_res')

RIPAT documentation built on Nov. 8, 2020, 6:24 p.m.