View source: R/Script_PLATE_08_DE_2_0_PlotDEValues.R
PlotDEValues | R Documentation |
Volcano plot of differential splicing and gene expression analysis results. This is a wrapper function for PlotDEValues.PSI.Mean
, PlotDEValues.Exp.Global
, and PlotDEValues.Exp.Spliced
.
PlotDEValues( MarvelObject, method = NULL, pval, level, delta = NULL, log2fc = NULL, psi.pval = NULL, psi.delta = NULL, gene.pval = NULL, gene.log2fc = NULL, point.size = 1, xlabel.size = 8, point.alpha = 1, anno = FALSE, anno.gene_short_name = NULL, anno.tran_id = NULL, label.size = 2.5, y.upper.offset = 5, event.types = c("SE", "MXE", "RI", "A5SS", "A3SS", "AFE", "ALE"), event.types.colors = NULL )
MarvelObject |
Marvel object. S3 object generated from |
method |
Character string. The statistical method used for differential splicing analysis. |
pval |
Numeric value. Only applicable when |
level |
Character string. Indicate |
delta |
Numeric value. Only applicable when |
log2fc |
Numeric value. Only applicable when |
psi.pval |
Numeric value. Only applicable when |
psi.delta |
Numeric value. Only applicable when |
gene.pval |
Numeric value. Only applicable when |
gene.log2fc |
Numeric value. Only applicable when |
point.size |
Numeric value. Size of data points. Default is |
xlabel.size |
Numeric value. Font size of the xtick labels. Default is |
point.alpha |
Numeric value. Only applicable when |
anno |
Logical value. If set to |
anno.gene_short_name |
Vector of character strings. When |
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 |
event.types |
Vector of character string(s). Only applicable when |
event.types.colors |
Vector of character string(s). Only applicable when |
An object of class S3 with new slot MarvelObject$DE$PSI$Plot[["method"]]
when level set to "splicing.mean"
or "splicing.distance"
or MarvelObject$DE$Exp.Global$Table
and MarvelObject$DE$Exp.Global$Plot
when level set to "gene.global"
or MarvelObject$DE$Exp.Spliced$Table
and MarvelObject$DE$Exp.Spliced$Plot
when level set to "gene.spliced"
.
marvel.demo <- readRDS(system.file("extdata/data", "marvel.demo.rds", package="MARVEL")) marvel.demo <- PlotDEValues(MarvelObject=marvel.demo, method="ad", pval=0.10, level="splicing.distance" ) # Check output marvel.demo$DE$PSI$Plot[["ad"]]
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