plot.GEandAScorrelation: Display results of correlation analyses

In nuno-agostinho/psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Display results of correlation analyses

Description

Plot, print and display as table the results of gene expression and alternative splicing

Usage

## S3 method for class 'GEandAScorrelation'
x[genes = NULL, ASevents = NULL]

## S3 method for class 'GEandAScorrelation'
plot(
  x,
  autoZoom = FALSE,
  loessSmooth = TRUE,
  loessFamily = c("gaussian", "symmetric"),
  colour = "black",
  alpha = 0.2,
  size = 1.5,
  loessColour = "red",
  loessAlpha = 1,
  loessWidth = 0.5,
  fontSize = 12,
  ...,
  colourGroups = NULL,
  legend = FALSE,
  showAllData = TRUE,
  density = FALSE,
  densityColour = "blue",
  densityWidth = 0.5
)

## S3 method for class 'GEandAScorrelation'
print(x, ...)

## S3 method for class 'GEandAScorrelation'
as.table(x, pvalueAdjust = "BH", ...)

Arguments

x	GEandAScorrelation object obtained after running correlateGEandAS()
genes	Character: genes
ASevents	Character: AS events
autoZoom	Boolean: automatically set the range of PSI values based on available data? If FALSE, the axis relative to PSI values will range from 0 to 1
loessSmooth	Boolean: plot a smooth curve computed by stats::loess.smooth?
loessFamily	Character: if gaussian, loess fitting is by least-squares, and if symmetric, a re-descending M estimator is used
colour	Character: points' colour
alpha	Numeric: points' alpha
size	Numeric: points' size
loessColour	Character: loess line's colour
loessAlpha	Numeric: loess line's opacity
loessWidth	Numeric: loess line's width
fontSize	Numeric: plot font size
...	Arguments passed on to stats::loess.smooth span smoothness parameter for loess. degree degree of local polynomial used. evaluation number of points at which to evaluate the smooth curve.
colourGroups	List of characters: sample colouring by group
legend	Boolean: show legend for sample colouring?
showAllData	Boolean: show data outside selected groups as a single group (coloured based on the colour argument)
density	Boolean: contour plot of a density estimate
densityColour	Character: line colour of contours
densityWidth	Numeric: line width of contours
pvalueAdjust	Character: method used to adjust p-values (see Details)

Details

The following methods for p-value adjustment are supported by using the respective string in the pvalueAdjust argument:

• none: do not adjust p-values

• BH: Benjamini-Hochberg's method (false discovery rate)

• BY: Benjamini-Yekutieli's method (false discovery rate)

• bonferroni: Bonferroni correction (family-wise error rate)

• holm: Holm's method (family-wise error rate)

• hochberg: Hochberg's method (family-wise error rate)

• hommel: Hommel's method (family-wise error rate)

Value

Plots, summary tables or results of correlation analyses

See Also

Other functions to correlate gene expression and alternative splicing: correlateGEandAS()

Other functions to correlate gene expression and alternative splicing: correlateGEandAS()

Examples

annot <- readFile("ex_splicing_annotation.RDS")
junctionQuant <- readFile("ex_junctionQuant.RDS")
psi <- quantifySplicing(annot, junctionQuant, eventType=c("SE", "MXE"))

geneExpr <- readFile("ex_gene_expression.RDS")
corr <- correlateGEandAS(geneExpr, psi, "ALDOA")

# Quick display of the correlation results per splicing event and gene
print(corr)

# Table summarising the correlation analysis results
as.table(corr)

# Correlation analysis plots
colourGroups <- list(Normal=paste("Normal", 1:3),
                     Tumour=paste("Cancer", 1:3))
attr(colourGroups, "Colour") <- c(Normal="#00C65A", Tumour="#EEE273")
plot(corr, colourGroups=colourGroups, alpha=1)

nuno-agostinho/psichomics documentation built on Feb. 11, 2024, 11:16 p.m.