plotCSCurve: Plots Cell Survival Curves

In PickeringLab/CellSurvAssay: Clonogenic Survival Analysis in R made easy!

Plots Cell Survival Curves

Description

This is one of the two functions that helps to plot the cell survival curves. It plots the curves, both for one cell type or multiple cell types, without having the user go through the data wrangling steps. It plots basic plots returned by the plot.cellsurvLQfit function. The recommended function for plotting the cell survival curves is the ggplotCSCurve, though, as it uses ggplot to plot the curves, and allows a lot of customization.

Usage

plotCSCurve(
  data,
  ...,
  method = "ml",
  PEmethod = "fit",
  col = NULL,
  xlim = NULL,
  ylim = c(0.008, 1),
  xlab = "Dose (Gy)",
  ylab = "Survival (1 = 100%)",
  title = NULL,
  pch = 1
)

Arguments

data	A data frame containing at least the following five columns: "cline", "Exp", "dose", "ncells", "ncolonies".
...	The name of the cell type(s)/group(s). If entering multiple cell types, separate each by a comma.
method	Method used for the fit. It's "ml" (maximum likelihood) by default. Can be "ls" (least squares) or "franken" (weighted least squares as described by Franken et al.(2006)).
PEmethod	Controls the value of the plating efficiencies. "fit" calculates fitted plating efficiencies as model parameters, "fix" uses fixed ones calculated from the observed zero dose.
col	A vector of strings denoting the colors of the curves. Size of the vector should be equal to the number of cell types entered.
xlim	A vector denoting the limits of x-axis.
ylim	A vector denoting the limits of y-axis.
xlab	A string denoting the label of x-axis.
ylab	A string denoting the label of y-axis.
title	A string denoting the title of the plot.
pch	An integer denoting the shape of the points in the plot.

Value

A plot object.

See Also

ggplotCSCurve

Examples

datatab <- CASP8_data

# Single curve

plotCSCurve(datatab, "control-B")

plotCSCurve(datatab, "control-NT", col = "blue", pch = 4, ylim = c(0.1, 1),
xlab = "X-axis", ylab = "Y-axis", title = "Curve of Control-NT")

# Multiple curves

plotCSCurve(datatab, "control-B", "control-NT")

plotCSCurve(datatab, "shCASP8-N", "shCASP8-B+Z+N", "control-B", col = c("red", "blue", "purple"),
pch = 4, ylim = c(0.1, 1), xlab = "X-axis", ylab = "Y-axis", title = "Multiple Curves")

PickeringLab/CellSurvAssay documentation built on June 15, 2022, 12:33 a.m.