plotInc: Plot a spatial inconsistency

In FisHiCal: Iterative FISH-based Calibration of Hi-C Data

Description

A function to plot a spatial inconsistency for a given loci (bin).

Usage

plotInc(i, neighborhoods, label = "fullName", size = 20, interactive = F)

Arguments

i	An integer giving the index of the loci (bin) for which the inconsistency graph should be plotted.
neighborhoods	The list of spatial inconsistencies detected by searchInc. 'neighborhoods' is a list where neighborhoods[i] gives the neighborhood of i, if a spatial inconsistency was detected for i, and NULL otherwise. Here, the neighborhood of i is the sub-graph of immediate neighbors in trans, an igraph object with attributes to label nodes by their name (index), fullName (chromosome name and genomic coordinates), membership (the connected component to which they belong, where i is always assigned with 0) and chr (chromosome name).
label	A character vector for labeling the nodes, set to "fullName" by default. Can be one of three options: "name"" (node index), "fullName"" (chromosome name and genomic coordinates) and "chr" (chromosome name). If not one of the above options, then nodes are labelled by their "name" attribute.
size	The size of the nodes in the plot, set to 20 by default. See searchInc for more details on plotting options.
interactive	A Boolean indicating whether the plot should be interactive or not. See searchInc for more details on plotting options.

Value

If the chosen neighborhood is not NULL, it is be plotted according to user preferences (nodes are colored by their connected component and labelled based on user choice).

Author(s)

Yoli Shavit

References

Y. Shavit, F.K. Hamey, P. Lio', FisHiCal: an R package for iterative FISH-based calibration of Hi-C data, 2014 (submitted).

See Also

searchInc
summaryInc

Examples

  data(spatialInc)
  plotInc(1, spatialInc) # no plot since no spatial incosistency was detected
  plotInc(167, spatialInc) 

FisHiCal documentation built on May 1, 2019, 10:09 p.m.