LDA_plot_activity: LDA_plot_activity

In LDAcoop: Analysis of Data from Limiting Dilution Assay (LDA) with or without Cellular Cooperation

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]])

LDAcoop documentation built on Sept. 12, 2024, 7:43 a.m.