R: Generate Score Violin Plot

scoreVlnplot

R Documentation

Generate Score Violin Plot

Description

scoreVlnplot generates a series of violin plots for visualizing the distribution of scores across different positions.

Usage

scoreVlnplot(
  data,
  savedir,
  pos.col = "position",
  wt.col = "wildtype",
  score.col = "mean",
  jitter = FALSE,
  c.fill = "lightblue",
  npos = 50,
  ncol = 1,
  pos.step = 1,
  x.text = 8,
  y.text = 8,
  seq.text = 3,
  pt.size = 0.2,
  ht = 30,
  wd = 15,
  name = "Violinplot",
  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`	A string providing the directory path to save plots.
`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`.
`score.col`	Column name in `data` for mutation scores. Default is `mean`.
`jitter`	Logical indicating whether to add jitter points to violin plot. Default is `FALSE`.
`c.fill`	String indicating the fill color for the violin plots.
`npos`	Integer specifying the number of positions per subplot. Default is `50`.
`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 `8`.
`y.text`	Numeric value for x-axis text size. Default is `8`.
`seq.text`	Numeric value for wildtype sequence text size. Default is `3`
`pt.size`	Numeric value specifying the size of jitter points. Default is `0.2`
`ht`	Numeric value for the height of the saved plot. Default is `30`.
`wd`	Numeric value for the width of the saved plot. Default is `15`.
`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: 
scoreVlnplot(data = scores.data, jitter = TRUE, c.fill = "lightpink",
            savedir = "./plots/", name = "ViolinPlot")

## End(Not run)