expressionAnalysisPlots: Plots for Analyzing Expression and Isoform Usage

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

Description

Together these three plots enables visualization of gene expression, isoform expression as well as isoform usage.

Usage

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switchPlotGeneExp(
    switchAnalyzeRlist,
    gene = NULL,
    condition1 = NULL,
    condition2 = NULL,
    addErrorbars = TRUE,
    confidenceIntervalErrorbars = TRUE,
    confidenceInterval = 0.95,
    alphas = c(0.05, 0.001),
    logYaxis=FALSE,
    extendFactor = 0.05,
    localTheme = theme_bw()
)

switchPlotIsoExp(
    switchAnalyzeRlist,
    gene=NULL,
    isoform_id = NULL,
    condition1 = NULL,
    condition2 = NULL,
    IFcutoff = 0.05,
    addErrorbars = TRUE,
    confidenceIntervalErrorbars = TRUE,
    confidenceInterval = 0.95,
    alphas = c(0.05, 0.001),
    logYaxis=FALSE,
    extendFactor = 0.05,
    localTheme = theme_bw()
)

switchPlotIsoUsage(
    switchAnalyzeRlist,
    gene=NULL,
    isoform_id = NULL,
    condition1 = NULL,
    condition2 = NULL,
    IFcutoff = 0.05,
    addErrorbars = TRUE,
    confidenceIntervalErrorbars = TRUE,
    confidenceInterval = 0.95,
    alphas = c(0.05, 0.001),
    extendFactor = 0.05,
    localTheme = theme_bw()
)

Arguments

switchAnalyzeRlist

A switchAnalyzeRlist object

gene

The gene_id or the gene name of the gene to plot. If not supplied 'isoform_id' must be supplied.

isoform_id

Vector of id indicating which isoforms (from the same gene) to plot. If not supplied 'gene' must be supplied.

condition1

First condition of the comparison to analyze. Must match 'condition_1' in the 'isoformFeatures' entry of the switchAnalyzeRlist. Only needed if more than one comparison is analyzed.

condition2

Second condition of the comparison to analyze. Must match 'condition_2' in the 'isoformFeatures' entry of the switchAnalyzeRlist. Only needed if more than one comparison is analyzed.

IFcutoff

The cutoff which the Isoform Fraction (IF) value (in at least one condition) must be larger than for a isoforms to be plotted. Default is 0.05 (which removes isoforms with minor contribution).

addErrorbars

A logic indicating whether error bars should be added to the expression plots to show uncertainty in estimates (recommended). Default is TRUE.

confidenceIntervalErrorbars

A logic indicating whether error bars should be given as confidence intervals (if TRUE)(recommended) or standard error of mean (if FALSE). Default is TRUE.

confidenceInterval

The confidence level used in the confidence intervals if confidenceIntervalErrorbars is enabled. Default is 0.95 corresponding to 95% (recommended).

alphas

A numeric vector of length two giving the significance levels represented in plots. The numbers indicate the q-value cutoff for significant (*) and highly significant (***) respectively. 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).

logYaxis

A logical indicating whether the y-axis of the plot should be log10 transformed (a pseudocount of 1 will be added to avid large negative values). Default is FALSE.

extendFactor

A numeric controlling the distance (as fraction of expression) between the bars indicating the expression values and the indications of significance. Default is 0.1

localTheme

General ggplo2 theme with which the plot is made, see ?ggplot2::theme for more info. Default is theme_bw().

Details

Changes in isoform usage are measure as the difference in isoform fraction (dIF) values, where isoform fraction (IF) values are calculated as <isoform_exp> / <gene_exp>.

Note that the bar indicating significance levels will only be shown if the analysis have been performed (if the q-values are not NA).

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

isoformSwitchTestDEXSeq
isoformSwitchTestDRIMSeq
switchPlotTranscript
switchPlot

Examples

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

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

### Plot expression
switchPlotGeneExp(
    exampleSwitchListAnalyzed,
    gene = mostSwitchingGene$gene_id,
    condition1 = mostSwitchingGene$condition_1,
    condition2 = mostSwitchingGene$condition_2
)

switchPlotIsoExp(
    exampleSwitchListAnalyzed,
    gene = mostSwitchingGene$gene_id,
    condition1 = mostSwitchingGene$condition_1,
    condition2 = mostSwitchingGene$condition_2
)

switchPlotIsoUsage(
    exampleSwitchListAnalyzed,
    gene = mostSwitchingGene$gene_id,
    condition1 = mostSwitchingGene$condition_1,
    condition2 = mostSwitchingGene$condition_2
)

kvittingseerup/IsoformSwitchAnalyzeR documentation built on May 12, 2021, 12:25 p.m.