plotConservationMatrix-methods: Plots a heatmap with the conservation score for each residue

In ddiez/motiftools: Tools to analyze sequence motifs

Description

Plots a heatmap with the conservation score for each residue colored according to the scheme shown in Jalview (htt://www.jalview.org).

Usage

plotConservationMatrix(x, ...)

## S4 method for signature 'matrix'
plotConservationMatrix(
  x,
  tree,
  raster = FALSE,
  tile.color = "transparent",
  show.tips = FALSE,
  show.consensus = FALSE,
  size = 8
)

## S4 method for signature 'AAMultipleAlignment'
plotConservationMatrix(
  x,
  tree,
  raster = FALSE,
  tile.color = "transparent",
  show.tips = FALSE,
  show.consensus = FALSE,
  size = 8
)

Arguments

x	a matrix as obtained with conservationMatrix() or an AAMultipleAlignment object.
...	arguments passed down to matrix-method.
tree	a tree of class dendrogram or that can be coerced into.
raster	logical; whether to use geom_raster (best for large alignments).
tile.color	color for the tile borders (default: transparent).
show.tips	logical; whether to show sequence ids.
show.consensus	logical; whether to show consensus sequence.
size	text size for consensus sequence.

Details

Sometimes computing the conservation matrix with conservationMatrix can be time consuming. In that case it might be better to store the output of conservationMatrix in a variable and pass that to plotConservationMatrix.

Examples

NULL

ddiez/motiftools documentation built on May 8, 2020, 11:38 a.m.