Chapter 5 Visualization

5.1 Learning Objectives

This chapter will cover:

Visualization in command line mode
Interactive visualization

5.1.1 Plot from command line

Chromosome wide plots:

> cnvpytor -root file.pytor -plot [rd BIN_SIZE] [likelihood BIN_SIZE] [baf BIN_SIZE] [snp] [-o IMAGE_FILENAME]

where * rd BIN_SIZE – plots RD signal for all chromosomes * likelihood BIN_SIZE – plots baf likelihood for all chromosomes * baf BIN_SIZE – plots baf/maf/likelihood peak position for all chromosomes * snp – plots baf for each snp for all chromosomes * -o IMAGE_FILENAME – if specified, saves plot in file instead to show on the screen

Manhattan plot:

> cnvpytor -root file.pytor -plot manhattan BIN_SIZE [-chrom name1 ...] [-o IMAGE_FILENAME]

Circular plot:

> cnvpytor -root file.pytor -plot circular BIN_SIZE [-chrom name1 ...] [-o IMAGE_FILENAME]

Plot genomic regions:

> cnvpytor -root file.pytor -plot regions [reg1[,| ]...] BIN_SIZE [-panels [rd] [likelihood] [baf] [snp] ...] [-o IMAGE_FILENAME]

where * reg1 – comma or space separated regions in form CHR[:START-STOP], e.g. 1:1M-20M 2 3:200k-80000010 * if regions are comma separated they will be plotted in the same subplot * space will split regions in different subplots * -panels – specify which panels to plot: rd likelihood baf snp * -o IMAGE_FILENAME – if specified, saves plot in file instead to show on the screen

5.1.2 Plot from interactive mode

The best way to visualize CNVpytor results is interactive mode. Enter interactive mode by typing:

cnvpytor -root file.pytor -view BIN_SIZE

There is tab completion and help similar to man pages. Type double tab or help to start.