PlotDEValues.PSI.Distance {MARVEL} | R Documentation |
Plot differential splicing analysis results based on distance statistics.
Description
Ranked plot for differential splicing analysis results based on distance statistics. Only statistical test that assess the overall PSI distribution between two cell groups will be eligible for plotting here, e.g., Anderson-Darling and DTS. x-axis represents the distance statistics. y-axis represents the adjusted p-values.
Usage
PlotDEValues.PSI.Distance(
MarvelObject,
method,
pval,
point.size = 1,
xlabel.size = 8,
anno = FALSE,
anno.tran_id = NULL,
label.size = 2.5,
y.upper.offset = 5
)
Arguments
MarvelObject |
Marvel object. S3 object generated from |
method |
Character string. The statistical method used for differential splicing analysis. |
pval |
Numeric value. Adjusted p-value below which the splcing events are considered as statistically significant and will consequently be color-annotated on the plot. |
point.size |
Numeric value. The point size for the data points. Default value is |
xlabel.size |
Numeric value. Font size of the xtick labels. Default is |
anno |
Logical value. If set to |
anno.tran_id |
Vector of character strings. When |
label.size |
Numeric value. Only applicable if |
y.upper.offset |
Numeric value. The value in -log10(p-value) to increase the upper limit of the y-axis. To be used when |
Value
An object of class S3 containing with new slot MarvelObject$DE$PSI$Plot[["method"]]
.
Examples
marvel.demo <- readRDS(system.file("extdata/data", "marvel.demo.rds", package="MARVEL"))
marvel.demo <- PlotDEValues.PSI.Distance(MarvelObject=marvel.demo,
method="ad",
pval=0.10
)
# Check output
marvel.demo$DE$PSI$Plot[["ad"]]