PlotDEValues {MARVEL}

Plot differential splicing and gene expression analysis results

Description

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.

Usage

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
)

Arguments

MarvelObject

Marvel object. S3 object generated from CompareValues function.

method

Character string. The statistical method used for differential splicing analysis.

pval

Numeric value. Only applicable when level set to "splicing.mean", "splicing.distance", and "gene.global". Adjusted p-value below which the splcing events or genes are considered as statistically significant and will consequently be color-annotated on the plot.

level

Character string. Indicate "splicing.distance" if the percent spliced-in (PSI) values' distribution was previously tested between 2 groups of cells using the CompareValues function. Statistical tests for distribution include Kolmogorov-Smirnov, Kuiper, and Anderson-Darling test. Indicate "splicing.mean" or gene if the PSI or gene expression values' mean was previously tested between 2 groups of cells using the CompareValues function. Statistical tests for comparing mean are t-test and Wilcoxon rank-sum test.

delta

Numeric value. Only applicable when level set to "splicing.mean". The positive (and negative) value specified above (and below) which the splicing events are considered to be statistically significant and will consequently be color-annotated on the plot.

log2fc

Numeric value. Only applicable when level set to "gene.global". The positive (and negative) value specified above (and below) which the genes are considered to be statistically significant and will consequently be color-annotated on the plot.

psi.pval

Numeric value. Only applicable when level set to "gene.spliced". The adjusted p-value from differential splicing analysis, below which, the splicing event is considered differentially spliced. Default is 0.1.

psi.delta

Numeric value. Only applicable when level set to "gene.spliced". The absolute differences in average PSI value between two cell groups from differential splicing analysis, above which, the splicing event is considered differentially spliced. Default is 0.

gene.pval

Numeric value. Only applicable when level set to "gene.spliced". The adjusted p-value from differential gene expression analysis, below which, the gene is considered differentially expressed. Default is 0.1.

gene.log2fc

Numeric value. Only applicable when level set to "gene.spliced". The absolute log2 fold change in gene expression betwene two cell groups from differential splicing analysis, above which, the gene is considered differentially expressed. Default is 0.5.

point.size

Numeric value. Size of data points. Default is 1.

xlabel.size

Numeric value. Font size of the xtick labels. Default is 8.

point.alpha

Numeric value. Only applicable when level set to "splicing.mean.g2vsg1". Transpancy of data points. Default is 1.

anno

Logical value. If set to TRUE, the specific gene names or splicing events will be annotated on the plot.

anno.gene_short_name

Vector of character strings. When anno set to TRUE, the gene names to be annotated on the plot.

anno.tran_id

Vector of character strings. When anno set to TRUE, the coordinates of the splicing events to be annotated on the plot.

label.size

Numeric value. Only applicable if anno set to TRUE. Size of the gene name labels.

y.upper.offset

Numeric value. The value in -log10(p-value) to increase the upper limit of the y-axis. To be used when anno set to TRUE so that gene labels will not be truncated at the upper limit of the y-axis.

event.types

Vector of character string(s). Only applicable when level set to "splicing.mean.g2vsg1". The specific splicing event to plot. May take any one or more of the following values "SE", "MXE", "RI", "A5SS", "A3SS", "AFE", and "ALE".

event.types.colors

Vector of character string(s). Only applicable when level set to "splicing.mean.g2vsg1". Customise colors as per splicing event type specified in event.types option. Should be of same length as event.types option.

Value

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".

Examples

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"]]