network {geneHapR}

Generate Haplotype Net Relationshop with Haplotype Result

Description

computes a haplotype network with haplotype summary result

Usage

get_hapNet(hapSummary,
           AccINFO = AccINFO,
           groupName = groupName,
           na.label = "Unknown")

getHapGroup(
  hapSummary,
  AccINFO = AccINFO,
  groupName = groupName,
  na.label = na.label
)

Arguments

hapSummary

object of hapSummary class, generated by hap_summary()

AccINFO

data.frame, specified groups of each accession. Used for pie plot. If missing, pie will not draw in plotHapNet. Or you can supplied a hap_group mattrix with plot(hapNet, pie = hap_group).

groupName

the group name used for pie plot, should be in AccINFO column names, default as the first column name

na.label

the label of NAs

Value

hapNet class

References

Mark P.J. van der Loo (2014) doi:10.32614/RJ-2014-011;

E. Paradis (2010) doi:10.1093/bioinformatics/btp696

See Also

plotHapNet() and hap_summary().

Examples

data("geneHapR_test")
hapSummary <- hap_summary(hapResult)

# calculate haploNet
hapNet <- get_hapNet(hapSummary,
                     AccINFO = AccINFO, # accession types
                     groupName = colnames(AccINFO)[2])

# plot haploNet
plot(hapNet)

# plot haploNet
plotHapNet(hapNet,
           size = "freq",   # circle size
           scale = "log10", # scale circle with 'log10(size + 1)'
           cex = 1, # size of hap symbol
           col.link = 2, # link colors
           link.width = 2, # link widths
           show.mutation = 2, # mutation types one of c(0,1,2,3)
           legend = FALSE) # legend position