plot.GEandAScorrelation: Display results of correlation analyses

Description Usage Arguments Details Value See Also Examples

View source: R/analysis_correlation.R

Description

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

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
## 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:

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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
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)

psichomics documentation built on Nov. 8, 2020, 5:44 p.m.