Make volcano plots

Construct interactive and non-interactive volcano plots, MA plots, STRING networks of up- and downregulated proteins, bar plots of average abundances and log-fold changes, as well as plots of top-ranked feature collections.

plotVolcano(
  sce,
  res,
  testType,
  xv = NULL,
  yv = NULL,
  xvma = NULL,
  volcind = NULL,
  plotnote = "",
  plottitle = "",
  plotsubtitle = "",
  volcanoFeaturesToLabel = c(""),
  volcanoMaxFeatures = 25,
  volcanoLabelSign = "both",
  baseFileName = NULL,
  comparisonString,
  groupComposition = NULL,
  stringDb = NULL,
  featureCollections = list(),
  complexFDRThr = 0.1,
  maxNbrComplexesToPlot = 10,
  curveparam = list(),
  abundanceColPat = "",
  xlab = "log2(fold change)",
  ylab = "-log10(p-value)",
  xlabma = "Average abundance",
  labelOnlySignificant = TRUE,
  interactiveDisplayColumns = NULL,
  interactiveGroupColumn = NULL,
  makeInteractiveVolcano = TRUE,
  maxTextWidthBarplot = NULL
)

Arguments

sce

A SummarizedExperiment object (or a derivative). Can be NULL if no "complex bar plots" are made (i.e., if featureCollections has no entry named "complexes", or if baseFileName is NULL).

res

A data.frame object with test results (typically generated by runTest).

testType

Character scalar indicating the type of test that was run, either "ttest", "limma" or "proDA".

xv, yv

Character scalars indicating which columns of res that should be used as the x- and y-axis of the volcano plot, respectively. If NULL, will be determined based on testType.

xvma

If not NULL, a character scalar indicating which column of res should be used as the x-axis for an MA plot. The y-axis column will be xv. If NULL, no MA plot is generated.

volcind

Character scalar indicating which column in res that represents the "significance" column. This should be a logical column; rows with a value equal to TRUE will be colored in the plot. If NULL, will be determined based on testType.

plotnote

Character scalar with a note to add to the plot.

plottitle

Character scalar giving the title of the plot.

plotsubtitle

Character scalar giving the subtitle of the plot.

volcanoFeaturesToLabel

Character vector, features to label in the plot.

volcanoMaxFeatures

Numeric scalar, the maximum number of features to color in the plot.

volcanoLabelSign

Character scalar, either "both", "pos", or "neg", indicating whether to label the most significant features regardless of sign, or only those with positive/negative log-fold changes.

baseFileName

Character scalar or NULL, the base file name of the output files. If NULL, no result files are generated.

comparisonString

Character scalar giving the name of the comparison of interest. This is used to extract the appropriate column from the metadata of the feature collections to make the gene set plots.

groupComposition

A list providing the composition of each group used in the comparisons indicated by comparisonString. If NULL, assumes that each group used in comparisonString consists of a single group in the group column of colData(sce).

stringDb

A STRINGdb object or NULL. If not NULL, STRING network plots of up- and downregulated genes will be added to the output pdf file.

featureCollections

A list of CharacterLists with feature collections. If there is a collection named "complexes", volcano plots and barplots for significant complexes are included in the output pdf files.

complexFDRThr

Numeric scalar giving the FDR threshold for complexes to be considered significant.

maxNbrComplexesToPlot

Numeric scalar, the largest number of significant complexes to generate separate volcano plots for.

curveparam

List with curve parameters for creating the Perseus-like significance curves in the volcano plots.

abundanceColPat

Character vector providing the column patterns used to identify abundance columns in the result table, to make bar plots for significant complexes. Typically the name of an assay.

xlab, ylab, xlabma

Character scalars giving the x- and y-axis labels to use for the volcano plots, and the x-axis label to use for the MA plot.

labelOnlySignificant

Logical scalar, whether to label only significant features (where volcind is TRUE), or to select the top volcanoMaxFeatures regardless of significance status.

interactiveDisplayColumns

Character vector (or NULL) indicating which columns of res to include in the tooltip for the interactive volcano plots. The default shows the feature ID.

interactiveGroupColumn

Character scalar (or NULL, default) indicating the column to group points by in the interactive volcano plot. Hovering over a point will highlight all other points with the same value of this column.

makeInteractiveVolcano

Logical scalar, indicating whether to construct an interactive volcano plot in addition to the static one.

maxTextWidthBarplot

Numeric scalar giving the maximum allowed width for text labels in the bar plot of log-fold changes. If not NULL, the size of the labels will be scaled down in an attempt to keep the labels inside the canvas. Typically set to half the width of the plot device (in inches).

Value

A list with plot objects. If baseFileName is not NULL, pdf files with volcano plots and bar plots for significant complexes will also be generated.

Author

Charlotte Soneson

Examples

sce <- readRDS(system.file("extdata", "mq_example", "1356_sce.rds",
                           package = "einprot"))
tres <- runTest(sce, comparisons = list(c("RBC_ctrl", "Adnp")),
                testType = "limma", assayForTests = "log2_LFQ.intensity",
                assayImputation = "imputed_LFQ.intensity")
pv <- plotVolcano(sce, tres$tests$Adnp_vs_RBC_ctrl, testType = "limma",
                  comparisonString = "Adnp_vs_RBC_ctrl")
#> Warning: Removed 39 rows containing missing values or values outside the scale range
#> (`geom_interactive_point()`).
pv$gg
#> Warning: Removed 39 rows containing missing values or values outside the scale range
#> (`geom_point()`).

pv$ggma
#> Warning: Removed 39 rows containing missing values or values outside the scale range
#> (`geom_point()`).

pv$ggwf