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)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(FisHiCal)
Loading required package: igraph
Attaching package: 'igraph'
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Loading required package: RcppArmadillo
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/FisHiCal/plotInc.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotInc
> ### Title: Plot a spatial inconsistency
> ### Aliases: plotInc
>
> ### ** Examples
>
> data(spatialInc)
> plotInc(1, spatialInc) # no plot since no spatial incosistency was detected
> plotInc(167, spatialInc)
This graph was created by an old(er) igraph version.
Call upgrade_graph() on it to use with the current igraph version
For now we convert it on the fly...
This graph was created by an old(er) igraph version.
Call upgrade_graph() on it to use with the current igraph version
For now we convert it on the fly...
This graph was created by an old(er) igraph version.
Call upgrade_graph() on it to use with the current igraph version
For now we convert it on the fly...
This graph was created by an old(er) igraph version.
Call upgrade_graph() on it to use with the current igraph version
For now we convert it on the fly...
This graph was created by an old(er) igraph version.
Call upgrade_graph() on it to use with the current igraph version
For now we convert it on the fly...
This graph was created by an old(er) igraph version.
Call upgrade_graph() on it to use with the current igraph version
For now we convert it on the fly...
This graph was created by an old(er) igraph version.
Call upgrade_graph() on it to use with the current igraph version
For now we convert it on the fly...
This graph was created by an old(er) igraph version.
Call upgrade_graph() on it to use with the current igraph version
For now we convert it on the fly...
This graph was created by an old(er) igraph version.
Call upgrade_graph() on it to use with the current igraph version
For now we convert it on the fly...
This graph was created by an old(er) igraph version.
Call upgrade_graph() on it to use with the current igraph version
For now we convert it on the fly...
This graph was created by an old(er) igraph version.
Call upgrade_graph() on it to use with the current igraph version
For now we convert it on the fly...
This graph was created by an old(er) igraph version.
Call upgrade_graph() on it to use with the current igraph version
For now we convert it on the fly...
>
>
>
>
>
> dev.off()
null device
1
>