dashboard: Draw dashboard for scoreset

In jweile/mavevis: Visualization for MaveDB

Draw dashboard for scoreset

Description

Retrieves a scoreset entry from MaveDB and renders a dashboard plot consisting of a genophenogram heatmap, interface burial, solvent accessibility, secondary structure and conservation. The output is controlled by the outFormats parameter and can be either on an X11 device or in PDF, SVG or PNG format (or any combination thereof). Structural and conservation information is obtained from UniProtKB and PDB, thus the respective database accessions are required. Multiple PDB files can be used at once.

Usage

dashboard(
  ssid,
  uniprotId = NULL,
  pdbs = NULL,
  mainChains = NULL,
  wt.seq = NULL,
  seq.offset = 0,
  syn.med = NULL,
  stop.med = NULL,
  overrideCache = FALSE,
  outFormats = c("pdf", "png"),
  pngRes = 100,
  outID = ssid,
  pixelMap = FALSE
)

Arguments

ssid	The MaveDB ScoreSet ID of the dataset to be visualized
uniprotId	The UniprotKB accession for the corresponding protein
pdbs	A vector of PDB accessions to be used for the structure tracks
mainChains	the chain identifiers corresponding to the protein in question for each provided pdb accession.
wt.seq	An (optional) wild-type sequence for the given protein to use instead of the sequence found in UniprotKB. This can be either a nucleotide or amino acid sequence.
seq.offset	A parameter describing the start position of the map in the protein's amino acid sequence. For example, if only a domain was scanned.
syn.med	The median value of synonymous variants as an estimate of wild-type function. This is only necessary of no synonymous variants are present in the dataset.
stop.med	The median value of nonsense variants as an estimate of complete loss of function. This is only necessary if no nonsense variants are present in the dataset.
overrideCache	defaults to FALSE. If set to TRUE, data will always be re-downloaded from remote locations instead of using a local cache.
outFormats	a vector containing any of the following strings: x11, svg, pdf, png . Using two or all three at once is allowed and will result in multiple output files.
pngRes	Resolution of PNG output in DPI. Defaults to 100.
outID	a name for the output file to which the plot will be written. Defaults to ssid.
pixelMap	boolean flag, whether to generate a pixel map for a png image. The map will be written to an Rdata file named according to the outID parameter. Defaults to FALSE.

Value

NULL.

Examples

## Not run: 
dashboard(
 ssid="urn:mavedb:00000001-a-1", uniprotId="P63279",
 pdbs="3UIP", mainChains="A",
  syn.med=1,stop.med=0
)

## End(Not run)

jweile/mavevis documentation built on Oct. 30, 2023, 7:16 a.m.