uclahs-cds / package-CancerEvolutionVisualization

Publication Quality Phylogenetic Tree Plots

https://cran.r-project.org/web/packages/CancerEvolutionVisualization/

GNU General Public License v2.0

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Standardized report input format #67

Open dan-knight opened 1 year ago

dan-knight commented 1 year ago

CEV

SRCGrob

`tree.df`	node.label	clone.id	parent	CP*	length_n*

`text.df`

Heatmaps

sample.id	snv.id	clone.id	CCF

SMC-Het

All files are tab separated with no headers. examples here

1A - Purity Estimation

1B - Number of Subclones

1C - Number of SNVs per Clone

clone.id	# of SNV	CP

2A - Hard SNV Assignment

SNV ID encodes more information, but must be unique.

sample.id	snv.id	ccf

snv.id	clone.id

2B - Soft SNV Assignment

3A - Binary Phylogeny

parent	clone.id

3B - Probabilistic Phylogeny