LDA_plot_activity {LDAcoop}

LDA_plot_activity

Description

generate clonogenic activity estimation plot (frequency of negative wells over the number of cells seeded) for data of limiting dilution assay (LDA) experiments. Input is an data object as returned by the preprocessing function LDA_prepare_plot().

Usage

LDA_plot_activity(LDA_obj, xlim = NULL, uncertainty.band = FALSE)

Arguments

LDA_obj

list returned from LDA_prepare_plot

xlim

manually setting the xlim

uncertainty.band

plotting uncertainty bands TRUE/FALSE

Value

none

Examples

x <- data.frame("cells" = rep(c(10,50,100,250),times = 4),
                "wells" = rep(25,16),
                "positive" = c(2,5,10,20,1,2,6,11,3,4,8,22,1,1,7,12),
                "group" = rep(c(rep("A",4),rep("B",4)),times = 2),
                "replicate" = c(rep(1,8),rep(2,8)))
out <- LDA_prepare_plot(x)
LDA_plot_activity(out[[1]])
data(LDAdata)
Z1 <- subset.data.frame(LDAdata,subset = name == unique(LDAdata$name)[1])
out <- LDA_prepare_plot(Z1[,c("S-value","# Tested","# Clonal growth",
                              "Group","replicate")])
LDA_plot_activity(out[[1]])