SNPratio_plot: SNP-ratio Wrapper Function

In EG-lisy/BSAvis: Bulk Segregant Analysis - Visualisation Package

Description

This wrapper function is used to fully run the SNP-ratio method, by calling all the funcitons involved in plotting the SNP-ratio values across positions of a specific chromosome.

SNPindex=AD_alt/(AD_ref + AD_alt)

Usage

SNPratio_plot(
  vcf.list,
  wtBulk,
  mBulk,
  variants = "SNP",
  min.SNPratio = 0.1,
  min.DP = 50,
  max.DP = 200,
  chrID,
  chr,
  degree = 2,
  span = 0.07,
  filename = paste0("plot_SNPratio_ch", chr),
  path = getwd(),
  dpi,
  width = 7.5,
  height = 5,
  units = "in"
)

Arguments

vcf.list	object containing meta information and vcf data frame
wtBulk	Wild-Type pool
mBulk	Mutant pool
variants	variants to be considered. Default is "SNP" (allowed: "SNP" or "all")
min.SNPratio	min value allowed for the SNP index (default=0.3)
min.DP	min value allowed for the read depth (default=50)
max.DP	max value allowed for the read depth (default=200)
chrID	chromosome ID of interest
chr	chromosome name printed on the plot
degree	LOESS smoothing degree (default=2)
span	LOESS smoothing span (default=0.07)
filename	file name under which the file will be saved (default="plot_SNPratio_chX")
path	path where the file will be saved (default=current working directory)
dpi	resolution value. If no value is given, plots will be generated but not saved
width	width value (default=7.5)
height	height value (default=5)
units	size units (default="in")

Details

Wrapper function that sequentially calls the required functions involved in generating the SNP-ratio plot: calc_SNPratio(), filter_SNPratio(), extract_chrIDs() and plot_SNPratio(). The resulting plot will show SNP-ratio values (for both bulks) across chromosome positions.

Examples

## Use default values WITHOUT saving the plot
SNPratio_plot(vcf.list=vcf_list, 
         wtBulk="pool_S3781_minus", 
         mBulk="pool_S3781_plus", 
         chrID="SL4.0ch03", 
         chr=3)
## OR use default values AND save the plot
SNPratio_plot(vcf.list=vcf_list, 
         wtBulk="pool_S3781_minus", 
         mBulk="pool_S3781_plus", 
         chrID="SL4.0ch03", 
         chr=3, 
         dpi=1200)
## OR customise default parameters
SNPratio_plot(vcf.list=vcf_list, 
         wtBulk="pool_S3781_minus", 
         mBulk="pool_S3781_plus", 
         variants="all",
         min.SNPratio=0.3, 
         min.DP=60, 
         max.DP=250,
         chrID="SL4.0ch03", 
         chr=3, 
         degree=1, 
         span=0.05, 
         filename="deltaSNPindex_chrom03", 
         path="Document/Plots", 
         dpi=1200, 
         width=20, 
         height=12, 
         units="cm")

EG-lisy/BSAvis documentation built on Dec. 17, 2021, 5:38 p.m.