Make pairs plot of selected assay from a SummarizedExperiment object

Construct a pairs plot of all columns of a given assay. The lower-triangular panels display the scatter plots, the upper-triangular ones print out the (Pearson or Spearman) correlations, and the diagonal panels show histograms of the respective columns.

Usage

plotPairs(
  se,
  selAssay = "counts",
  doLog = TRUE,
  pseudocount = 1,
  corMethod = "pearson",
  histBreaks = 40,
  pointsType = "points",
  corSizeMult = 5,
  corSizeAdd = 2,
  pointSize = 0.1,
  pointAlpha = 0.3,
  colorByCorrelation = TRUE,
  corrColorRange = NULL,
  addIdentityLine = FALSE
)

Arguments

se

A SummarizedExperiment object, e.g. the output of summarizeExperiment

selAssay

Character scalar, the assay to use as the basis for the pairs plot.

doLog

Logical scalar, whether or not to log-transform the values before plotting.

pseudocount

Numeric scalar, the pseudocount to add to the values before log-transforming (if doLog is TRUE).

corMethod

Either "pearson" or "spearman", the type of correlation to calculate.

histBreaks

Numeric scalar, the number of breaks in the histograms to put in the diagonal panels.

pointsType

Either "points" or "smoothscatter", determining the type of plots that will be made.

corSizeMult, corSizeAdd

Numeric scalars determining how the absolute correlation value is transformed into a font size. The transformation is corSizeMult * abs(corr) + corSizeAdd.

pointSize, pointAlpha

Numeric scalars determining the size and opacity of points in the plot.

colorByCorrelation

Logical scalar, indicating whether the correlation panels should be colored according to the correlation value.

corrColorRange

Numeric vector of length 2, providing the lower and upper limits of the color scale when coloring by correlation. Both values should be positive; the same range is used for negative correlations. If NULL (the default), the range is inferred from the data.

addIdentityLine

Logical scalar, indicating whether the identity line should be added (only used if pointsType = "points").

Value

A ggplot object.

Author

Charlotte Soneson

Examples

se <- readRDS(system.file("extdata", "GSE102901_cis_se.rds", 
                          package = "mutscan"))[1:200, ]
plotPairs(se)