switchPlotTranscript: Plot Transcript Structure and Annoation

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/isoform_plots.R

Description

This function plots the transcript structure of all (or selected) isoforms from a gene along with all the annotation added to the switchAnalyzeRlist including transcript classification, ORF, Coding Potential, NMD sensitivity, annotated protein domains as well as annotated signal peptides.

Usage

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switchPlotTranscript(
    switchAnalyzeRlist,
    gene = NULL,
    isoform_id = NULL,
    rescaleTranscripts = TRUE,
    plotXaxis = !rescaleTranscripts,
    reverseMinus = TRUE,
    ifMultipleIdenticalAnnotation = "summarize",
    annotationImportance = c('signal_peptide','protein_domain','idr'),
    IFcutoff = 0.05,
    rectHegith = 0.2,
    codingWidthFactor = 2,
    nrArrows = 20,
    arrowSize = 0.2,
    optimizeForCombinedPlot = FALSE,
    condition1 = NULL,
    condition2 = NULL,
    dIFcutoff = 0.1,
    alphas = c(0.05, 0.001),
    localTheme = theme_bw(),
    plot = TRUE
)

Arguments

switchAnalyzeRlist

A switchAnalyzeRlist object where the ORF is annotated (for example via analyzeORF).

gene

Either the gene_id or the gene name of the gene to plot, alternatively one can use the isoform_id argument to supply a vector of isoform_ids.

isoform_id

A vector of the id(s) of which isoform(s) (from the same gene) to plot, alternatively one can use the gene_id argument to plot all isoforms of a gene.

rescaleTranscripts

A Logical indicating whether all the isoforms should be rescaled to the squareroot of their original sizes. This feature is implemented because introns usually are much larger than exons making it difficult to see structural changes. This is very usefull for structural visualization but the scaling might distort actual intron and exon sizes. Default is TRUE.

plotXaxis

A logical indicating whether x-axis should be shown. Default is the opposite of the rescaleTranscripts (meaning FALSE when rescale is TRUE and vice versa).

reverseMinus

A logic indicating whether isoforms on minus strand should be inverted so they are visualized as going from left to right instead of right to left. (Only affects minus strand isoforms). Default is TRUE

ifMultipleIdenticalAnnotation

This argument determines how to visually handle if multiple instances of the same domain is found, the options are A) \'summarize\' which will assign one color to all the domains (and adding the number of domains in a bracket in the legend). B) \'number\' which will add a number to each domain and give each domain a seperate color. Default is \'summarize\'. C) \'ignore\' which will cause IsoformSwitchAnalyzeR to just plot all of them in the same color but without highlighting differences in numbers.

annotationImportance

Since some of the annotation collected potentially overlap (mainly protein domains and IDR) but only one can be visualized this argument controls the importance of the respective annotations. Must be a vector of strings indicating the order of the annotations in decreasing importance. All annotation must be mentioned even if they have not been analyzed. Default is c('signal_peptide','protein_domain','idr') which means that if an IDR and a protein domain overlap the protein domain will be visualized.

IFcutoff

The cutoff used for the minimum contribution to gene expression (in at least one condition) for an isoforms must have to be plotted (measured as Isoform Fraction (IF) values). Default is 0.05 (which removes isoforms with minor contribution).

rectHegith

When drawing the transcripts what should be the size of the non-coding (and UTR) regions (if the total height of a transcript is larger than 1 they start to overlap).

codingWidthFactor

The number deciding the width of the coding regions compared to the non-coding (as a fraction of the non-coding). A number larger than 1 will result in coding regions being thicker than non-coding regions.

nrArrows

An integer controlling the number of arrows drawn in the intron of transcripts. Given as the number of arrows a hypothetical intron spanning the whole plot window should have (if you get no arrows increase this value). Default is 20.

arrowSize

The size of arrowhead drawn in the intron of transcripts. Default is 0.2

optimizeForCombinedPlot

A logic indicating whether to optimize for use with switchPlot(). Default is FALSE

condition1

First condition of the comparison to analyze must be the name used in the switchAnalyzeRlist. If specified text indicating change in isoform usage is also added to the plot.

condition2

Second condition of the comparison to analyze, must be the name used in the switchAnalyzeRlist. If specified text indicating change in isoform usage is also added to the plot.

dIFcutoff

The dIF cutoff used to add usage to the transcript plot. Only considered if both condition1 and condition2 are defined. Default is 0.1.

alphas

A numeric vector of length two giving the significance levels represented in the usage text added to the plot. The numbers indicate the q-value cutoff for significant (*) and highly significant (***) respecitively. Only considered if both condition1 and condition2 are defined. Default is 0.1. Default 0.05 and 0.001 which should be interpret as q<0.05 and q<0.001 respectively). If q-values are higher than this they will be annotated as 'ns' (not significant).

localTheme

General ggplot2 theme with which the plot is made, see ?ggplot2::theme for more info. Default is theme_bw().

plot

A Logical indicating whether the final plot should be plotted (TRUE) or returned (FALSE). Default is TRUE.

Details

This function generates a plot visualizing all the annotation for the transcripts gathered. The plot supports visualization of:

Value

Author(s)

Kristoffer Vitting-Seerup

References

Vitting-Seerup et al. The Landscape of Isoform Switches in Human Cancers. Mol. Cancer Res. (2017).

See Also

analyzeORF
analyzeCPAT
analyzePFAM
analyzeSignalP

Examples

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### Prepare for plotting
data("exampleSwitchListAnalyzed")

mostSwitchingGene <- extractTopSwitches(
    exampleSwitchListAnalyzed,
    filterForConsequences = TRUE,
    n = 1
)

### Plot transcript structure
switchPlotTranscript(exampleSwitchListAnalyzed, gene = mostSwitchingGene$gene_id)

kvittingseerup/IsoformSwitchAnalyzeR documentation built on July 20, 2019, 8:54 a.m.