genBaRcode: createGDF – R documentation

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createGDF

Creating a gdf File

Description

createGDF creates a data file usable with the free graph visualisation tool gephi. The nodes represent barcodes and its respective size reflects the corresponding read counts. Edges between nodes indicate a distance between two barcodes of maximal minD. If ori_BCs is provided the node color refelects the distance of a particular barcode to one of the provided barcode sequences.

Usage

createGDF(
  BC_dat,
  minDist = 1,
  loga = TRUE,
  ori_BCs = NULL,
  col_type = "rainbow",
  m = "hamming"
)

Arguments

`BC_dat`	a BCdat object.
`minDist`	an integer value representing the maximal distance value for which the graph will contain edges.
`loga`	a logical value indicating the use or non-use of logarithmic read count values.
`ori_BCs`	a vector of character strings containing the barcode sequences (without the fixed positions of the barcode construct).
`col_type`	character sting, choosing one of the available color palettes.
`m`	a character string, Method for distance calculation, default value is Hamming distance. Possible values are "osa", "lv", "dl", "hamming", "lcs", "qgram", "cosine", "jaccard", "jw", "soundex" (see stringdist function of the stringdist-package for more information).

Examples

## Not run: 

data(BC_dat)
createGDFFile(BC_dat, minDist = 1, loga = TRUE, ori_BCs = NULL, col_type = "rainbow")


## End(Not run)

genBaRcode

Analysis and Visualization Tools for Genetic Barcode Data

v1.2.4

LGPL

Authors

Lars Thielecke <lars.thielecke@tu-dresden.de>

Initial release