plotLfcGC-methods {exomePeak2} | R Documentation |
plotLfcGC
plot the scatter plot between GC content and the (differential) modification LFCs.
plotLfcGC( sep, bsgenome = NULL, txdb = NULL, save_pdf_prefix = NULL, point_size = 0.05, xlim = c(0.2, 0.9), fragment_length = 100, binding_length = 25, effective_GC = FALSE, save_dir = "." ) ## S4 method for signature 'SummarizedExomePeak' plotLfcGC( sep, bsgenome = NULL, txdb = NULL, save_pdf_prefix = NULL, point_size = 0.05, xlim = c(0.2, 0.9), fragment_length = 100, binding_length = 25, effective_GC = FALSE, save_dir = "." )
sep |
a |
bsgenome |
a |
txdb |
a |
save_pdf_prefix |
a |
point_size |
a |
xlim |
a |
fragment_length |
a |
binding_length |
a |
effective_GC |
a |
save_dir |
a |
By default, this function will generate a scatter plot between GC content and the log2FC value. The significant modification sites will be lebeled in different colours.
a ggplot
object.
### Load the example SummarizedExomPeak object f1 = system.file("extdata", "sep_ex_mod.rds", package="exomePeak2") sep <- readRDS(f1) ### Visualize the relationship between GC content and the (differential) LFC plotLfcGC(sep)