plotPairs: Make pairs plot of selected assay from a SummarizedExperiment...

In fmicompbio/mutscan: Preprocessing and Analysis of Deep Mutational Scanning Data

Make pairs plot of selected assay from a SummarizedExperiment object

Description

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(s)

Charlotte Soneson

Examples

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

fmicompbio/mutscan documentation built on Nov. 18, 2024, 11:42 p.m.