seismic graph

Purpose

seismic graph creates plots from mutation rate tables and/or predicted structures. It is a group of subcommands, each producing a different plot type.

Subcommands

Run seismic graph {subcommand} --help for each subcommand’s full option list.

Subcommand	Description
`profile`	Bar graph of mutation rate (or other relationship) per position
`delprof`	Bar graph of the difference between two profiles per position
`scatter`	Scatter plot comparing two profiles
`corroll`	Rolling correlation between two profiles
`giniroll`	Rolling Gini coefficient along a profile
`snrroll`	Rolling signal-to-noise ratio along a profile
`aucroll`	Rolling AUC-ROC comparing a profile to a predicted structure
`histpos`	Histogram of relationship values across positions
`histread`	Histogram of relationship values across reads
`mutdist`	Distribution of distances between mutations within reads
`poscorr`	Correlation between pairs of positions
`roc`	ROC curve comparing a mutation rate profile to a structure
`abundance`	Bar graph of cluster abundances

Inputs

Table CSV files, fold CT files, or output directories: Subcommands that compare two datasets accept two sets of inputs. See Specify Input Files.

Outputs

{graph-type}.html: Interactive HTML plot (viewable in any web browser).
{graph-type}.svg or {graph-type}.png: Static image (depending on options).

Outputs go into {out}/{sample}/graph/{ref}/{reg}/.

Quick example

Plot mutation rate profiles for all filter outputs:

seismic graph profile out/

Compare two profiles:

seismic graph scatter out/sample-1/filter/ref-1 out/sample-2/filter/ref-1

Options

Common options shared by all graph subcommands include:

--rels CODES (-r): Which relationship(s) to graph (e.g. m for mutated, n for unambiguous; default m).
--use-ratio / --use-count: Graph ratios (e.g. mutation rates) or raw counts (default: --use-ratio).
--graph-quantile F: Normalize and winsorize ratios to this quantile before graphing (default 0.0, i.e. no normalization).
--cgroup {c|k|a}: Put each cluster in its own file (c), each number of clusters K in its own file (k), or all clusters in one file (a).
--html / --no-html: Write an interactive HTML plot (default on).
--svg / --png / --pdf: Also write static SVG, PNG, and/or PDF images (default off).
--csv / --no-csv: Also write the graphed data as a CSV file (default on).
--force: Overwrite existing outputs.

See the auto-generated Command Line Reference for the complete per-subcommand option lists.