... As you have used *_ratio.txt*, each dot represents the predicted copy number for each window.
The size of the window will depend on your input configuration file.
My own selection / collection:
control procedures for genome-wide association studies
- Data quality
control in genetic case-control association studies (credit: alessandrotestori7)
General GWAS / genetic studies
comprehensive re ...
... You can infer tumour and normal samples via the TCGA barcode: https://www.biostars.org/p/313063/#313066
... Yet another answer, via *biomaRt*, in R: