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GenomeSpy

Generates an RMarkdown report, which displays genomic regions or copy number segmentations using GenomeSpy.

This component exposes a simplified GenomeSpy API and is limited to displaying only one type of data at a time. Two different visualization methods are available for encoding region-specific variables:

If the dataset consists of multiple samples, the sample parameter must be defined.

Read more about GenomeSpy at https://github.com/tuner/genome-spy

Version 1.0
Bundle microarray
Categories
Authors Kari Lavikka (kari.lavikka@helsinki.fi)
Issue tracker View/Report issues
Requires R ; GenomeSpy (R-package) ; rmarkdown (R-package)
Source files component.xml GenomeSpy.Rmd GenomeSpy.R
Usage Example with default values

Inputs

Name Type Mandatory Description
in CSV Mandatory A CSV file containing at least the genomic coordinates (chromosome, start, end). The file may contain additional columns, which can be encoded by the provided visualization methods.
samples CSV Optional

An optional CSV file that specifies the order of the samples and optional display names for them. The file should contain at least a sample column. The sample names can be substituted by including a label column. However, note that substitution is not a proper mean for anonymization. The original names are still available in the produced HTML source and visible by hovering the segments with mouse.

In future, this file may also contain additional sample-specific variables such as clinical data. Current version of GenomeSpy does not support that, though.

Outputs

Name Type Description
out HTMLFile An HTML document with a self-contained GenomeSpy and the data.

Parameters

Name Type Default Description
baf string "" Applies to cnvVis: the column containing B-allele frequencies. The variable is visualized as loss of heterozygosity, which is more meaningful and easier to perceive in the visualization.
chrom string (no default) Name of the chromosome column. The chromosome names may optionally contain the chr prefix, i.e. both X and chrX are equally valid.
color string "" Applies to simpleVis: the column that is used for coloring the regions.
end string (no default) The column that contains the intra-chromosomal end position of the region.
genome string (no default) The genome assembly to use, for example hg19 or hg38.
sample string "" The column that is used for spreading the data to multiple tracks, e.g. sample or patient identifiers.
seg string "" Applies to cnvVis: the column containing segmentation means.
start string (no default) The column that contains the intra-chromosomal start position of the region.
title string "Results" The title of the resulting HTML document.

Test cases

Test case Parameters IN
in
IN
samples
OUT
out
ascat properties in (missing) (missing)

genome=hg38,
sample=sample,
chrom=chr,
start=startpos,
end=endpos,
seg=segMean,
baf=bafMean

color properties in (missing) (missing)

genome=hg38,
chrom=chr,
start=start,
end=end,
color=x

custom_sample_order properties in samples (missing)

genome=hg38,
chrom=Chr,
start=Start,
end=End,
sample=Case,
seg=segMean,
baf=bafMean

seg_baf_color properties in (missing) (expecting failure)

genome=hg38,
chrom=chr,
start=start,
end=end,
color=a,
seg=b,
baf=c

trivial_example properties in (missing) (missing)

genome=hg38,
chrom=chr,
start=start,
end=end


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