plot.mlst: Plot A mlst Object
In iferres/quickMLST: Quick Multi Locus Sequence Typing Analisys

Description Usage Arguments Details Value

View source: R/methods_mlst.R

Plot a mlst object. A Minimum Spanning Tree or a binary tree is rendered.

## S3 method for class 'mlst'
plot(
  x,
  type = "mst",
  what = "both",
  pt.size = 3,
  label = FALSE,
  pf.col = "#E64B35FF",
  st.col = "#00A087FF",
  nst.col = "white",
  alpha = 0.5,
  pairwise.deletion = FALSE,
  plot.igraph.args = list(),
  plot.phylo.args = list(),
  tiplabels.args = list(),
  plot = TRUE,
  ...
)

`x`	An object of class `mlst`.
`type`	One of "mst" or "phylo", for plotting a Minimum Spanning Tree or a binary tree.
`what`	One of "result", "profile", "both" (default). What should be plotted.
`pt.size`	The size of the point. Default: 3.
`label`	`logical`. Whether to plot node/tip labels or not. Default: `FALSE`.
`pf.col`	The color of profile nodes/tips. Ignored if `what="result"`.
`st.col`	The color of result nodes/tips which have an ST assigned. Ignored if `what="profile"`.
`nst.col`	The color of result nodes/tips with no ST assigned. Default: `"white"`. Ignored if `what="profile"`.
`alpha`	Color transparency, between [0,1]. See alpha.
`pairwise.deletion`	A `logical` indicating whether to delete the comumns with missing data on a pairwise basis. If `FALSE` (default) and `NA`s are found, then each `NA` is condidered as a different allele when computing distance.
`plot.igraph.args`	A `list` of arguments to be passed to plot.igraph. Used only if `type="mst"`. Defaults try to keep aesthetics similar to `phylo`'s. Default: `list(vertex.label = if (label) NULL else NA, vertex.size = pt.size)`.
`plot.phylo.args`	A `list` of arguments to be passed to plot.phylo. Used only if `type="phylo"`. Defaults try to keep aesthetics similar to `mst`'s. Default: `list(type='unrooted', show.tip.label = label)`.
`tiplabels.args`	A `list` of arguments to be passed to tiplabels. Used only if `type="phylo"`. Defaults try to keep aesthetics similar to `mst`'s. Default: `list(pch = 21, cex = pt.size/5)`.
`plot`	Default: TRUE.
`...`	A list of arguments to be passed to par.

Distance is calculated using dist.gene function over the allele matrix. This distance metric only takes into account the number of differences between each pair of rows in the matrix. If type="mst", mst function is used to calculate a minimum spanning tree, and a graph is generated using graph.adjacency. If type="phylo", a "phylogeny" is inferred using the distance calculated above and nj function (neighbour-joining tree). Ethier a igraph or a phylo object is returned invisibly so it can be further analysed using igraph/ape frameworks.

It is worth noting that the result of this function is not strictly based on genetic information. The distance used just counts the number of differences on the allele profiles, it doesn't use a genetic model. The clustering methods are also simple and are not based on complex evolution models. Despite the above, since alleles in mlst schemes usually differ in 1 or few nucleotides, the described methodology gives good enough results to have a general overview of your data.

A minimum spanning tree plot and an object of class igraph (invisible) if type="mst", or a binary tree plot and an object of class phylo (invisible) if type="phylo".

iferres/quickMLST documentation built on Dec. 22, 2020, 5:10 p.m.