Draw_lego: The tool is used to plot lego image for mutation spectrum

In BGI-LuoWen/lwlegopt: luo wen's lego-plot tool

Description

The tool is used to plot lego image for mutation spectrum.

Usage

Draw_lego(
         h=NULL,         # Data matrix for plot lego, [96 x (n+2), n stands for sample counts] 
	 path=NULL,      # The directory of input file.
	 file_name=NULL, # The name of input file 
     	 title=NULL,     # Cancer name 	 
	 prepare=FALSE,  # Prophase data prepare  
     	 samtools=NULL,  # Samtools software,if prepare id TRUE, the parameter must be set
	 fasta=NULL,	 # Genome of human,if prepare id TRUE, the parameter must be set
     	 sort=NULL,      # Sort for trinucleotide percentage value
	 top=TRUE,       # Location of icon displaying
	 kge=3,          # Scale interval of Y axis 
	 color=NULL      # colours for lego figure
	 border=NULL     # colours for border

Arguments

h	Data matrix for plot lego
path	Data path
file_name	Name of input file
title	Cancer type
prepare	Prophase data prepare for the results detected by mutect
samtools	Samtools software
fasta	Genome of human
sort	Sort for trinucleotide percentage value, TRUE,FALSE and NULL
top	Location of icon displaying,TRUE,FALSE
kge	Scale interval of Y axis
color	colours for lego figure
border	colours for border

Examples

####### 1 #########
library(lwlegopt)
data(Mutdata)
Draw_lego(h)

####### 2 #########
library(lwlegopt)
Draw_lego(path="example",file_name='TCGA.originalGenomes_with_types.txt')

####### 3 #########
library(lwlegopt)
Draw_lego(path="example",file_name='combined_mutations.out.xls',title='CRC',prepare=TRUE,samtools='/usr/bin/samtools/samtools',fasta='/usr/Database/human_19/hg19_fasta_GATK/hg19.fasta')

BGI-LuoWen/lwlegopt documentation built on May 5, 2019, 10:25 a.m.