R: Generate Score Heatmap

scoreHeatmap

R Documentation

Generate Score Heatmap

Description

scoreHeatmap generates a series of heatmaps for visualizing the score patterns across different positions.

Usage

scoreHeatmap(
  data,
  savedir,
  ctrl.name = "synonymous",
  pos.col = "position",
  wt.col = "wildtype",
  mut.col = "mutation",
  type.col = "type",
  score.col = "mean",
  aa.order = NA,
  npos = 100,
  ncol = 1,
  pos.step = 5,
  x.text = 6,
  y.text = 3,
  seq.text = 1.1,
  c.pallete = "RdBu",
  c.scale = list(),
  ht = 11,
  wd = 8.5,
  name = "Heatmap",
  savepdf = TRUE,
  show = FALSE
)

Arguments

`data`	Scores data frame. Expected to have columns containing information about position, control amino acid, mutated amino acid, mutation type, and score.
`savedir`	Character string specifying the directory to save plots.
`ctrl.name`	String specifying the control mutation name. Default is `synonymous`.
`pos.col`	Column name in `data` for mutation positions. Default is `position`.
`wt.col`	Column name in `data` for wildtype amino acids. Default is `wildtype`.
`mut.col`	Column name in `data` for mutated amino acids. Default is `mutation`.
`type.col`	Column name in `data` for mutation types. Default is `type`.
`score.col`	Column name in `data` for mutation scores. Default is `mean`.
`aa.order`	Character vector defining the order of amino acid mutations in the y-axis. Default to using mutations from `data` in alphabetical order.
`npos`	Integer specifying the number of positions per subplot. Default is `100`.
`ncol`	Integer specifying the number of columns of subplots. Default is `1`.
`pos.step`	Integer specifying the steps between x-axis labels. Default is `5`.
`x.text`	Numeric value for x-axis text size. Default is `6`.
`y.text`	Numeric value for y-axis text size. Default is `3`.
`seq.text`	Numeric value for wildtype sequence text size. Default is `1.1`
`c.pallete`	Character string or vector defining the color palette. Default is `'RdBu'`.
`c.scale`	List of parameters definning the score color scale.
`ht`	Numeric value for the height of the saved plot. Default is `11`.
`wd`	Numeric value for the width of the saved plot. Default is `8.5`.
`name`	Character string specifying the base name of the saved file.
`savepdf`	Logical indicating whether to also save a PDF version of the plot. Default is `TRUE`.
`show`	Logical indicating whether or not to display the plot in the viewer. Default is `FALSE`.

Value

NULL.

Examples

## Not run: 
scoreHeatmap(scores.data, savedir = "./plots/", name = "Heatmap", savepdf = TRUE)

## End(Not run)