| plot_normalization {DEP} | R Documentation |
plot_normalization generates boxplots
of all conditions for input objects, e.g. before and after normalization.
plot_normalization(se, ...)
se |
SummarizedExperiment,
Data object, e.g. before normalization (output from |
... |
Additional SummarizedExperiment object(s),
E.g. data object after normalization
(output from |
Boxplots of all conditions
for input objects, e.g. before and after normalization
(generated by ggplot).
Adding components and other plot adjustments can be easily done
using the ggplot2 syntax (i.e. using '+')
# Load example
data <- UbiLength
data <- data[data$Reverse != "+" & data$Potential.contaminant != "+",]
data_unique <- make_unique(data, "Gene.names", "Protein.IDs", delim = ";")
# Make SummarizedExperiment
columns <- grep("LFQ.", colnames(data_unique))
exp_design <- UbiLength_ExpDesign
se <- make_se(data_unique, columns, exp_design)
# Filter and normalize
filt <- filter_missval(se, thr = 0)
norm <- normalize_vsn(filt)
# Plot normalization
plot_normalization(se, filt, norm)