PlotSynergy {synergyfinder}R Documentation

Drug interaction landscape

Description

A function to visualize the synergy scores for drug combinations as 2D or 3D interaction landscape over the dose-response matrix.

Usage

PlotSynergy(
  data,
  type = "2D",
  save.file = FALSE,
  pair.index = NULL,
  len = 3,
  legend.start = NULL,
  legend.end = NULL,
  legend.lab.cex = 1,
  row.range = NULL,
  col.range = NULL,
  color.low.value = "green",
  main.title.cex = 1,
  axis.lab.cex = 0.8,
  axis.title.cex = 1,
  color.high.value = "red",
  file.name = NULL,
  file.type = "pdf",
  height = NULL,
  width = 12
)

Arguments

data

a list object generated by function CalculateSynergy.

type

a parameter to specify the type of the interaction landscape, 2D, 3D or both. By default, 2D interaction landscape is returned.

save.file

a logical parameter to specify if the interaction landscape is saved as a pdf file in the current working directory or returned as an R object. By default, it is FALSE.

pair.index

a parameter to specify which drug combination if there are many drug combinations in the data. By default, it is NULL so that the synergy score visualization of all the drug combinations in the data is returned.

len

a parameter to specify how many values need to be predicted between two concentrations. It is used to control the smoothness of the synergy surface in the plot.

legend.start

a parameter to specify the starting point of the legend. By defualt, it is NULL so the legend starting point is fixed by the data automatically.

legend.end

a parameter to specify the ending point of the legend. By defualt, it is NULL so the legend ending point is fixed by the data automatically.

legend.lab.cex

a numeric value. The magnification to be used for legend labels.

row.range

a parameter to specify the starting and ending concentration of the drug on y-axis. Use e.g., c(1, 3) to specify that only from 1st to 3rd concentrations of the drug on y-axis are used. By default, it is NULl so all the concentrations are used.

col.range

a parameter to specify the starting and ending concentration of the drug on x-axis. Use e.g., c(1, 3) to specify that only from 1st to 3rd concentrations of the drug on x-axis are used. By default, it is NULl so all the concentrations are used.

color.low.value

a charactor in R color format. It indicates the color for the synergy score lower than 0. Default setting is "green".

main.title.cex

a numeric value. The magnification to be used for axis annotation.

axis.lab.cex

a numeric value. The magnification to be used for x, y and z axis labels.

axis.title.cex

a numeric value. The magnification to be used for main titles.

color.high.value

a charactor in R color format. It indicates the color for the synergy score higher than 0. Default setting is "red".

file.name

a character vector. It indicates the file names, if user chose to save the plot to local directory.If it is not defined by user, a default name will be assigned.

file.type

a character. It indicates the format of files you want to save as. Default is "pdf". Available values are "jpeg", "bmp", "png", "tiff", "pdf", "svg".

height

a numeric value. It indicates the height of the output plot. If it is NULL (default setting), it will be automatically set according to the width and type parameters. If the type is "all", height = width, otherwise height = width/2.

width

a numeric value. It indicates the width of the output plot.

Value

a numeric value. It is the summarized synergy score.

Author(s)

Examples

data("mathews_screening_data")
data <- ReshapeData(mathews_screening_data)
scores <- CalculateSynergy(data)
PlotSynergy(scores, "2D")
PlotSynergy(scores, "3D", save.file = TRUE, file.name = c("plot1", "plot2"))

[Package synergyfinder version 2.2.4 Index]