Plots a heatmap with the conservation score for each residue — plotConservationMatrix • motiftools

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

plotConservationMatrix(x, ...)

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

# S4 method for 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
#> NULL