expressionAnalysisPlots: Plots for Analyzing Expression and Isoform Usage
In IsoformSwitchAnalyzeR: Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.

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

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

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()
)

`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().

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).

switchPlotGeneExp : Generates a gene expression plot which also indicates whether the gene are differentially expressed between the two conditions
switchPlotIsoExp : Generates a isoform expression plot which also indicates whether the isoforms are differentially expressed between the two conditions
switchPlotIsoUsage : Plots the changes in isoform usage (given by IF the values) along with the significance of the change in isoform usage of each isoform. Requires that the result of a differential isoform usage analysis have been performed (for example via isoformSwitchTestDEXSeq).

Kristoffer Vitting-Seerup

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

isoformSwitchTestDEXSeq
isoformSwitchTestDRIMSeq
switchPlotTranscript
switchPlot

### 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
)