siRNAPlot {synlet} | R Documentation |
Plot the normalized RNAi screen data, row data, control signals and Z' factor.
siRNAPlot(gene, dat, controlsiRNA, FILEPATH = ".", colour = rainbow(10), zPrimeMed, zPrimeMean, treatment, control, normMethod = c("PLATE"), width = 15, height = 14)
gene |
gene symbol, case sensitive |
dat |
synthetic lethal RNAi screen data |
controlsiRNA |
controlsiRNA could be a vector of several siRNA, including postive/negative control |
FILEPATH |
path to store the figure |
colour |
colour used in graphs |
zPrimeMed |
zPrime factor basing on median |
zPrimeMean, |
zPrime factor basing on mean |
treatment |
the treatment condition in EXPERIMENT_MODIFICATION |
control |
the control condition in EXPERIMENT_MODIFICATION |
normMethod |
could be a PLATE and negative controls |
width |
width of the plot |
height |
height of the plot |
Return the ggplot2 objects in a list, which could be plotted individually.
zF_mean <- zFactor(exampleDat, negativeCon = "scrambled control si1", positiveCon = "PLK1 si1") zF_med <- zFactor(exampleDat, negativeCon = "scrambled control si1", positiveCon = "PLK1 si1", useMean = FALSE) tem.1 <- siRNAPlot("AAK1", exampleDat, controlsiRNA = c("lipid only", "scrambled control si1"), FILEPATH = ".", zPrimeMed = zF_med, zPrimeMean = zF_mean, treatment = "treatment", control = "control", normMethod = c("PLATE", "lipid only", "scrambled control si1"))