plotPrevalence {miaViz}

R Documentation

Plot prevalence information

Description

plotPrevalence and plotTaxaPrevalence visualize prevalence information.

Usage

plotPrevalence(x, ...)

## S4 method for signature 'SummarizedExperiment'
plotPrevalence(
  x,
  detections = c(0.01, 0.1, 1, 2, 5, 10, 20)/100,
  prevalences = seq(0.1, 1, 0.1),
  abund_values = "counts",
  as_relative = TRUE,
  rank = NULL,
  BPPARAM = BiocParallel::SerialParam(),
  ...
)

plotPrevalentAbundance(x, ...)

## S4 method for signature 'SummarizedExperiment'
plotPrevalentAbundance(
  x,
  rank = taxonomyRanks(x)[1L],
  abund_values = "counts",
  as_relative = TRUE,
  colour_by = NULL,
  size_by = NULL,
  shape_by = NULL,
  label = NULL,
  facet_by = NULL,
  ...
)

plotTaxaPrevalence(x, ...)

## S4 method for signature 'SummarizedExperiment'
plotTaxaPrevalence(
  x,
  rank = taxonomyRanks(x)[1L],
  abund_values = "counts",
  detections = NULL,
  ndetections = 20,
  as_relative = TRUE,
  min_prevalence = 0,
  BPPARAM = BiocParallel::SerialParam(),
  ...
)

Arguments

x	a SummarizedExperiment object.
detections	Detection thresholds for absence/presence. Either an absolutes value compared directly to the values of x or a relative value between 0 and 1, if as_relative = TRUE.
prevalences	Prevalence thresholds (in 0 to 1). The required prevalence is strictly greater by default. To include the limit, set include_lowest to TRUE.
abund_values	a character value defining which assay data to use. (default: abund_values = "relabundance")
as_relative	logical scalar: Should the detection threshold be applied on compositional (relative) abundances? Passed onto getPrevalence. (default: TRUE)
rank, ...	additional arguments If !is.null(rank) matching arguments are passed on to agglomerateByRank. See ?agglomerateByRank for more details. additional arguments for plotting. See mia-plot-args for more details i.e. call help("mia-plot-args")
BPPARAM	A BiocParallelParam object specifying whether the UniFrac calculation should be parallelized.
colour_by	Specification of a feature to colour points by, see the by argument in ?retrieveFeatureInfo for possible values. Only used with layout = "point".
size_by	Specification of a feature to size points by, see the by argument in ?retrieveFeatureInfo for possible values. Only used with layout = "point".
shape_by	Specification of a feature to shape points by, see the by argument in ?retrieveFeatureInfo for possible values. Only used with layout = "point".
label	a logical, character or integer vector for selecting labels from the rownames of x. If rank is not NULL the rownames might change. (default: label = NULL)
facet_by	Taxonomic rank to facet the plot by. Value must be of taxonomyRanks(x) Argument can only be used in function plotPrevalentAbundance.
ndetections	If detections is NULL, a number of breaks are calculated automatically. as_relative is then also regarded as TRUE.
min_prevalence	a single numeric value to apply as a threshold for plotting. The threshold is applied per row and column. (default: min_prevalence = 0)

Details

Whereas plotPrevalence procudes a line plot, plotTaxaPrevalence returns a heatmap.

Agglomeration on different taxonomic levels is available through the rank argument.

To exclude certain taxa, preprocess x to your liking, for example with subsetting via getPrevalentTaxa or agglomerateByPrevalence.

Value

A ggplot2 object or plotly object, if more than one prevalences was defined.

See Also

getPrevalence, agglomerateByPrevalence, agglomerateByRank

Examples

data(GlobalPatterns, package = "mia")

# plotting N of prevalence exceeding taxa on the Phylum level
plotPrevalence(GlobalPatterns, rank = "Phylum")
plotPrevalence(GlobalPatterns, rank = "Phylum") + scale_x_log10()

# plotting prevalence per taxa for different detectio thresholds as heatmap
plotTaxaPrevalence(GlobalPatterns, rank = "Phylum")

# by default a continous scale is used for different detections levels, 
# but this can be adjusted
plotTaxaPrevalence(GlobalPatterns, rank = "Phylum",
                   detections = c(0, 0.001, 0.01, 0.1, 0.2))
                   
# point layout for plotTaxaPrevalence can be used to visualize by additional
# information
plotPrevalentAbundance(GlobalPatterns, rank = "Family",
                       colour_by = "Phylum") +
    scale_x_log10()

# When using function plotPrevalentAbundace, it is possible to create facets
# with 'facet_by'.
plotPrevalentAbundance(GlobalPatterns, rank = "Family",
                       colour_by = "Phylum", facet_by = "Kingdom") +
    scale_x_log10()

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