5. Visualization - abyzovlab/CNVpytor GitHub Wiki

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

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.

Examples

>cnvpytor -root file.pytor -view 10000

cnvpytor> Manhattan
cnvpytor> chr1:1M-50M
cnvpytor> set panels rd likelihood
cnvpytor> Manhattan
cnvpytor> set chrom chr1
cnvpytor> Manhattan
cnvpytor> set chrom chr1 chr2
cnvpytor> Manhattan