plotLGDistances – plots a heatmap of the distances between linkage groups
Description
plotLGDistances – plots a heatmap of the distances between linkage groups
Usage
## S4 method for signature 'LinkageGroupList,StrandStateMatrix'
plotLGDistances(object,
allStrands, lg = "all", labels = TRUE)
Arguments
object
LinkageGroupList
allStrands
StrandStateMatrix for all linkageGroups (usually reoriented by reorientStrandTable)
lg
='all' vector of integers to determine which linkage group(s) to plot. 'all' will calculate consensus
strand calls for all linkage groups and plot them side by side (default it 'all')
labels
=TRUE if TRUE, contig names will be plotted on the axes
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(contiBAIT)
Loading required package: BH
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/contiBAIT/plotLGDistances-LinkageGroupList-StrandStateMatrix-method.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotLGDistances,LinkageGroupList,StrandStateMatrix-method
> ### Title: plotLGDistances - plots a heatmap of the distances between
> ### linkage groups
> ### Aliases: plotLGDistances
> ### plotLGDistances,LinkageGroupList,LinkageGroupList-method
> ### plotLGDistances,LinkageGroupList,StrandStateMatrix-method
>
> ### ** Examples
>
> data("exampleLGList")
> data("exampleWCMatrix")
>
> plotLGDistances(exampleLGList, exampleWCMatrix)
> plotLGDistances(exampleLGList, exampleWCMatrix, lg=1)
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.
