Generate score histograms/density plots by mutation type

generates a density plot for visualizing the distribution of scores across different mutation types (same as Rosace scoreDensity function)

Usage

lilace_score_density(
  data,
  savedir,
  type.col = "type",
  score.col = "mean",
  hist = FALSE,
  nbins = 30,
  c.fill = c("#FF7575", "lightgreen", "#7298BF"),
  alpha = 0.5,
  x.text = 10,
  y.text = 10,
  scale.free = FALSE,
  space.free = FALSE,
  ht = 10,
  wd = 8,
  name = "DensityPlot",
  savepdf = TRUE,
  savesvg = FALSE,
  show = TRUE
)

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.

type.col

Column name in `data` for mutation types. Default is `type`.

score.col

Column name in `data` for mutation scores. Default is `mean`.

hist

Logical indicating whether to plot count histogram or density. Default is `FALSE`.

nbins

Numeric value specifying the number of bins for the histogram. Default is `30`.

c.fill

Vector indicating the fill color for mutation types.

alpha

Numeric value between 0-1 indicating the fill transparency. Default is `0.5`

x.text

Numeric value for x-axis text size. Default is `10`.

y.text

Numeric value for x-axis text size. Default is `10`.

scale.free

Logical indicating whether to make score range proportional. Default is `FALSE`.

space.free

Logical indicating whether to make panel heights variable. Default is `FALSE`.

ht

Numeric value for the height of the saved plot. Default is `10`.

wd

Numeric value for the width of the saved plot. Default is `8`.

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`.

savesvg

logical indicating whether to save as svg

show

Logical indicating whether or not to display the plot in the viewer. Default is `TRUE`.

Value

NULL.

Examples

if (FALSE) { # \dontrun{
lilace_score_density(scores, output_dir, score.col="effect",
                     name="score_histogram", hist=T, scale.free=T)
} # }