net_growth_rate: net_growth_rate

In Michorlab/ACESO: A Cancer Evolution Simulation Optimizer

Description

Function to calculate the net growth rate from the cell viability assay data.

Usage

net_growth_rate(Inputdata, death_rate = NULL, birth_rate = NULL,
  time0_data = T)

Arguments

Inputdata	name of the dataframe where the cell viability data is saved.
death_rate	numeric value for the death rate. Default to NULL.
birth_rate	numeric value for the birth rate. Default to NULL.
time0_data	logical argument to specify if the cell viability data for time 0 values should be used or not. Default to TRUE.

Value

The Inputdata dataframe with the net growth rate values for each cell type added.

Examples

## Not run: 
data(Dactolisib_Trametinib_combination)
growth_data<-net_growth_rate(Dactolisib_Trametinib_combination)
library(ggplot2)
ggplot(data=growth_data,aes(x=(CONC),y=Net_growth,col=factor(CONC2)))+geom_point()+
geom_line(linetype="dashed")+
theme(text = element_text(size=14))+xlab(expression(paste("[Dactolisib] (",mu,"M)", sep="")))+
scale_colour_discrete(name=expression(paste("[Trametinib] (",mu,"M)", sep="")))+
theme_classic()+ylab("Net growth (1/h)")
 
#Calculate the birth rate from the net growth rate assuming a death of 0.021 1/h
###Needed for dataset with more than 1 cell line
d0=vector("list", length = length(unique(growth_data$Cell.line))) 
###To identify each death rate with the name of the cell line
names(d0)=unique(as.character(growth_data$Cell.line)) 
###Introduce the value of 0.021 1/h
d0[[1]]=0.021
growth_data<-net_growth_rate(growth_data,death_rate = d0)

ggplot(data=growth_data,aes(x=(CONC),y=Birth_rate,col=factor(CONC2)))+geom_point()+
geom_line(linetype="dashed")+
theme(text = element_text(size=14))+xlab(expression(paste("[Dactolisib] (",mu,"M)", sep="")))+
scale_colour_discrete(name=expression(paste("[Trametinib] (",mu,"M)", sep="")))+
theme_classic()+ylab("Birth rate (1/h)")

## End(Not run)

Michorlab/ACESO documentation built on June 4, 2021, 4:57 p.m.