PlotDoseResponseCurve: Plot Dose Response Curve for Single Drug

In shuyuzheng/synergyfinder: Calculate and Visualize Synergy Scores for Drug Combinations

Plot Dose Response Curve for Single Drug

Description

This function will pot the dose response curve fitted by 4 parameters log-logistic curve.

Usage

PlotDoseResponseCurve(
  data,
  plot_block = 1,
  drug_index = 1,
  adjusted = TRUE,
  Emin = NA,
  Emax = NA,
  grid = TRUE,
  point_color = "#C24B40",
  curve_color = "black",
  text_size_scale = 1,
  plot_title = NULL,
  plot_subtitle = NULL,
  plot_setting = list(cex.lab = 1 * text_size_scale, mgp = c(2, 0.5, 0), font.main = 2,
    font.lab = 1, cex.main = 14/12 * text_size_scale, bty = "l", lwd = 1.5),
  plot_new = TRUE,
  record_plot = TRUE,
  ...
)

Arguments

data	A list object generated by function ReshapeData.
plot_block	A character/integer. It indicates the block ID for the block to visualize.
drug_index	A character/integer. It indicates the index of the drug to plot. For example, 1 or "1" indicates to plot "drug1" in the input data.
adjusted	A logical value. If it is FALSE, original response value will be used to fit the curve. If it is TRUE, the response values adjusted by (adding noise and/or imputation) will be plotted.
Emin	A numeric or NA. the minimal effect of the drug used in the 4-parameter log-logistic function to fit the dose-response curve. If it is not NA, it is fixed the value assigned by the user. Default setting is NA.
Emax	A numeric or NA. the maximal effect of the drug used in the 4-parameter log-logistic function to fit the dose-response curve. If it is not NA, it is fixed the value assigned by the user. Default setting is NA.
grid	A logical value. It indicates whether to show the grids in the plots. The default value is TRUE. If grid = NULL or grid = FALSE, there is no grid.
point_color	An R color value. It indicates the color for points in dose response curve plots.
curve_color	An R color value. It indicates the color for curves in dose response curve plots.
text_size_scale	A numeric value. It is used to control the size of text in the plot. All the text size will multiply by this scale factor.
plot_title	A character value or NULL. It specifies the plot title. If it is NULL, the function will automatically generate a title.
plot_subtitle	A character or NULL. It indicates the subtitle for the plot. If it is NULL, the function will automatically generate a subtitle.
plot_setting	A list of graphical arguments. The arguments are passed to par function to modify the appearance of plots.
plot_new	A logic value. If it is TRUE, a new device will be initiate with plot.new. You might want to set it as FALSE while combining with other plots by using layout function.
record_plot	A logic value. If it is TRUE, a plot object recorded by recordPlot will be returned. If it is FALSE, this function will return NULL.
...	Additional graphical arguments that are inherited from link[drc]plot.drc function. For example, use xlim = c(0.5, 500) or ylim = (0, 100) to control the ranges of x-axis or y-axis, respectively.

Value

A plot object recorded by recordPlot or NULL.

Author(s)

• Shuyu Zheng [e-mail]

• Jing Tang [e-mail]

Examples

data("mathews_screening_data")
data <- ReshapeData(mathews_screening_data)
p <- PlotDoseResponseCurve(data, plot_block = 1, drug_index = 2, grid = NULL)
replayPlot(p)

shuyuzheng/synergyfinder documentation built on Feb. 20, 2023, 11:33 p.m.