Up: Component summary
Up: Component summary
Component
MutationContextPlotDraws mutation context plots for sequencing samples. Samples can be included as an array where each individual file corresponds to a sample or as a single csv file. Inputs should contain the minimal number of columns to minimize memory load.
| Version | 0.1 |
|---|---|
| Bundle | sequencing |
| Categories | Plot |
| Authors | Riku Louhimo (Riku.Louhimo@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Requires | R ; SomaticSignatures (R-package) ; VariantAnnotation (R-package) ; ggplot2 (R-package) ; BSgenome.Hsapiens.UCSC.hg18 (R-package) ; BSgenome.Hsapiens.UCSC.hg19 (R-package) ; BSgenome.Hsapiens.UCSC.hg38 (R-package) |
| Source files | component.xml MutationContextPlot.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| array | Array<CSV> | Optional | Array of CSV files containing the mutation information. Array keys are used as sample names. |
| in | CSV | Optional | CSV file containing mutation information for one or more samples. Must contain columns for mutation locus, reference and alternative alleles, and sample. Columns are defined using 'dataCols' and 'sampleCol' parameters. |
Outputs| Name | Type | Description |
|---|---|---|
| plot | Latex | Latex folder containing the mutation context spectra barplots. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| build | string | (no default) | Genome build of the sample(s). One of 'hg18', 'hg19' or 'hg38'. This is only used to determine the length of chromosomes so don't worry if your samples have been aligned to the Ensembl version of the reference genome. |
| dataCols | string | (no default) | Comma-separated list of column names containing the chromosome, locus, reference and alternative allele of the variants. Notice that the order of values is significant and assumed to be 'CHR,LOCUS,ALT,REF'. |
| sampleBySample | boolean | true | Plot all samples in one plot or every sample in an individual plot. Defaults to individual plots. Ignored if input is an array. |
| sampleCol | string | "" | Name of the column containing sample names. Ignored if array input is used. |
Test cases| Test case | Parameters▼ | IN array |
IN in |
OUT plot |
||
|---|---|---|---|---|---|---|
| case1 | properties | (missing) | in | (missing) | ||
|
dataCols=Chr,Locus,Ref,Alt, |
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| case2 | properties | array | (missing) | (missing) | ||
|
dataCols=Chr,Locus,Ref,Alt, |
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