plotTree: Plotting tree information enriched with information

In microbiome/miaViz: Microbiome Analysis Plotting and Visualization

Plotting tree information enriched with information

Description

Based on the stored data in a TreeSummarizedExperiment a tree can be plotted. From the rowData, the assays as well as the colData information can be taken for enriching the tree plots with additional information.

Usage

plotRowTree(object, ...)

plotColTree(object, ...)

## S4 method for signature 'TreeSummarizedExperiment'
plotColTree(
  object,
  tree_name = "phylo",
  relabel_tree = FALSE,
  order_tree = FALSE,
  remove_levels = FALSE,
  show_label = FALSE,
  show_highlights = FALSE,
  show_highlight_label = FALSE,
  abbr_label = FALSE,
  add_legend = TRUE,
  layout = "circular",
  edge_colour_by = NULL,
  edge_size_by = NULL,
  tip_colour_by = NULL,
  tip_shape_by = NULL,
  tip_size_by = NULL,
  node_colour_by = NULL,
  node_shape_by = NULL,
  node_size_by = NULL,
  colour_highlights_by = NULL,
  by_exprs_values = "counts",
  other_fields = list(),
  ...
)

## S4 method for signature 'TreeSummarizedExperiment'
plotRowTree(
  object,
  tree_name = "phylo",
  relabel_tree = FALSE,
  order_tree = FALSE,
  remove_levels = FALSE,
  show_label = FALSE,
  show_highlights = FALSE,
  show_highlight_label = FALSE,
  abbr_label = FALSE,
  add_legend = TRUE,
  layout = "circular",
  edge_colour_by = NULL,
  edge_size_by = NULL,
  tip_colour_by = NULL,
  tip_shape_by = NULL,
  tip_size_by = NULL,
  node_colour_by = NULL,
  node_shape_by = NULL,
  node_size_by = NULL,
  colour_highlights_by = NULL,
  by_exprs_values = "counts",
  other_fields = list(),
  ...
)

Arguments

object	a TreeSummarizedExperiment object.
...	additional arguments for plotting. See mia-plot-args for more details i.e. call help("mia-plot-args")
tree_name	a single character value specifying a rowTree/colTree from object. (By default: tree_name = "phylo")
relabel_tree	logical scalar, Should the tip labels be relabeled using the output of getTaxonomyLabels(object, with_rank = TRUE)? (default: relabel_tree = FALSE)
order_tree	logical scalar, Should the tree be ordered based on alphabetic order of taxonomic levels? (default: order_tree = FALSE)
remove_levels	logical scalar, Should taxonomic level information be removed from labels? (default: relabel_tree = FALSE)
show_label, show_highlights, show_highlight_label, abbr_label	logical (scalar), integer or character vector. If a logical scalar is given, should tip labels be plotted or if a logical vector is provided, which labels should be shown? If an integer or character vector is provided, it will be converted to a logical vector. The integer values must be in the range of 1 and number of nodes, whereas the values of a character vector must match values of the label column in the node data. In case of a character vector only values corresponding to actual labels will be plotted and if no labels are provided no labels will be shown. (default: FALSE)
add_legend	logical scalar. Should legends be plotted? (default: add_legend = TRUE)
layout	layout for the plotted tree. See ggtree for details.
edge_colour_by	Specification of a column metadata field or a feature to colour tree edges by, see the by argument in ?retrieveCellInfo for possible values.
edge_size_by	Specification of a column metadata field or a feature to size tree edges by, see the by argument in ?retrieveCellInfo for possible values.
tip_colour_by	Specification of a column metadata field or a feature to colour tree tips by, see the by argument in ?retrieveCellInfo for possible values.
tip_shape_by	Specification of a column metadata field or a feature to shape tree tips by, see the by argument in ?retrieveCellInfo for possible values.
tip_size_by	Specification of a column metadata field or a feature to size tree tips by, see the by argument in ?retrieveCellInfo for possible values.
node_colour_by	Specification of a column metadata field or a feature to colour tree nodes by. Must be a field from other_fields.
node_shape_by	Specification of a column metadata field or a feature to shape tree nodes by. Must be a field from other_fields.
node_size_by	Specification of a column metadata field or a feature to size tree nodes by. Must be a field from other_fields.
colour_highlights_by	Should the highlights be colour differently? If show_highlights = TRUE, colour_highlights will be set to TRUE as default. (default: colour_highlights = FALSE)
by_exprs_values	A string or integer scalar specifying which assay to obtain expression values from, for use in point aesthetics - see the exprs_values argument in ?retrieveCellInfo.
other_fields	Additional fields to include in the node information without plotting them.

Details

If show_label or show_highlight_label have the same length as the number of nodes, the vector will be used to relabel the nodes.

Value

a ggtree plot

See Also

splitByRanks

Examples

library(scater)
library(mia)
# preparation of some data
data(GlobalPatterns)
altExps(GlobalPatterns) <- splitByRanks(GlobalPatterns)
altExp(GlobalPatterns,"Genus") <- addPerFeatureQC(altExp(GlobalPatterns,"Genus"))
rowData(altExp(GlobalPatterns,"Genus"))$log_mean <-
  log(rowData(altExp(GlobalPatterns,"Genus"))$mean)
rowData(altExp(GlobalPatterns,"Genus"))$detected <-
   rowData(altExp(GlobalPatterns,"Genus"))$detected / 100
top_genus <- getTopFeatures(altExp(GlobalPatterns,"Genus"),
                        method="mean",
                        top=100L,
                        assay.type="counts")
#
x <- altExp(GlobalPatterns,"Genus")
plotRowTree(x[rownames(x) %in% top_genus,],
            tip_colour_by = "log_mean",
            tip_size_by = "detected")

# plot with tip labels
plotRowTree(x[rownames(x) %in% top_genus,],
            tip_colour_by = "log_mean",
            tip_size_by = "detected",
            show_label = TRUE)
# plot with selected labels
labels <- c("Genus:Providencia", "Genus:Morganella", "0.961.60")
plotRowTree(x[rownames(x) %in% top_genus,],
            tip_colour_by = "log_mean",
            tip_size_by = "detected",
            show_label = labels,
            layout="rectangular")

# plot with labeled edges
plotRowTree(x[rownames(x) %in% top_genus,],
            edge_colour_by = "Phylum",
            tip_colour_by = "log_mean")
# if edges are sized, colours might disappear depending on plotting device
plotRowTree(x[rownames(x) %in% top_genus,],
            edge_colour_by = "Phylum",
            edge_size_by = "detected",
            tip_colour_by = "log_mean")

# aggregating data over the taxonomic levels for plotting a taxonomic tree
# please note that the original tree of GlobalPatterns is dropped by
# unsplitByRanks
altExps(GlobalPatterns) <- splitByRanks(GlobalPatterns)
top_phyla <- getTopFeatures(altExp(GlobalPatterns,"Phylum"),
                        method="mean",
                        top=10L,
                        assay.type="counts")
altExps(GlobalPatterns) <- lapply(altExps(GlobalPatterns), addPerFeatureQC)
altExps(GlobalPatterns) <-
   lapply(altExps(GlobalPatterns),
          function(y){
              rowData(y)$log_mean <- log(rowData(y)$mean)
              rowData(y)$detected <- rowData(y)$detected / 100
              y
          })
x <- unsplitByRanks(GlobalPatterns)
x <- addHierarchyTree(x)

highlights <- c("Phylum:Firmicutes","Phylum:Bacteroidetes",
                "Family:Pseudomonadaceae","Order:Bifidobacteriales")
plotRowTree(x[rowData(x)$Phylum %in% top_phyla,],
            tip_colour_by = "log_mean",
            node_colour_by = "log_mean",
            show_highlights = highlights,
            show_highlight_label = highlights,
            colour_highlights_by = "Phylum")

plotRowTree(x[rowData(x)$Phylum %in% top_phyla,],
            edge_colour_by = "Phylum",
            edge_size_by = "detected",
            tip_colour_by = "log_mean",
            node_colour_by = "log_mean")

microbiome/miaViz documentation built on April 21, 2024, 8:45 a.m.