plotTree: Plotting tree information enriched with information
In microbiome/miaViz: Microbiome Analysis Plotting and Visualization
plotTree R Documentation
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(x, ...)
plotColTree(x, ...)
## S4 method for signature 'TreeSummarizedExperiment'
plotColTree(
x,
tree.name = tree_name,
tree_name = "phylo",
relabel.tree = relabel_tree,
relabel_tree = FALSE,
order.tree = order_tree,
order_tree = FALSE,
levels.rm = remove_levels,
remove_levels = FALSE,
show.label = show_label,
show_label = FALSE,
show.highlights = show_highlights,
show_highlights = FALSE,
show.highlight.label = show_highlight_label,
show_highlight_label = FALSE,
abbr.label = abbr_label,
abbr_label = FALSE,
add.legend = add_legend,
add_legend = TRUE,
layout = "circular",
edge.colour.by = edge.colour.by,
edge_colour_by = NULL,
edge.size.by = edge_size_by,
edge_size_by = NULL,
tip.colour.by = tip_colour_by,
tip_colour_by = NULL,
tip.shape.by = tip_shape_by,
tip_shape_by = NULL,
tip.size.by = tip_size_by,
tip_size_by = NULL,
node.colour.by = node_colour_by,
node_colour_by = NULL,
node.shape.by = node_shape_by,
node_shape_by = NULL,
node.size.by = node_size_by,
node_size_by = NULL,
colour.highlights.by = colour_highlights_by,
colour_highlights_by = NULL,
assay.type = by_exprs_values,
by_exprs_values = "counts",
other.fields = other_fields,
other_fields = list(),
...
)
## S4 method for signature 'TreeSummarizedExperiment'
plotRowTree(
x,
tree.name = tree_name,
tree_name = "phylo",
relabel.tree = relabel_tree,
relabel_tree = FALSE,
order.tree = order_tree,
order_tree = FALSE,
levels.rm = remove_levels,
remove_levels = FALSE,
show.label = show_label,
show_label = FALSE,
show.highlights = show_highlights,
show_highlights = FALSE,
show.highlight.label = show_highlight_label,
show_highlight_label = FALSE,
abbr.label = abbr_label,
abbr_label = FALSE,
add.legend = add_legend,
add_legend = TRUE,
layout = "circular",
edge.colour.by = edge_colour_by,
edge_colour_by = NULL,
edge.size.by = edge_size_by,
edge_size_by = NULL,
tip.colour.by = tip_colour_by,
tip_colour_by = NULL,
tip.shape.by = tip_shape_by,
tip_shape_by = NULL,
tip.size.by = tip_size_by,
tip_size_by = NULL,
node.colour.by = node_colour_by,
node_colour_by = NULL,
node.shape.by = node_shape_by,
node_shape_by = NULL,
node.size.by = node_size_by,
node_size_by = NULL,
colour.highlights.by = colour_highlights_by,
colour_highlights_by = NULL,
assay.type = by_exprs_values,
by_exprs_values = "counts",
other.fields = other_fields,
other_fields = list(),
...
)
Arguments
x
a
TreeSummarizedExperiment
x.
...
additional arguments for plotting. See
mia-plot-args for more details i.e. call help("mia-plot-args")
tree.name
Character scalar. Specifies a rowTree/colTree from
x. (Default: tree.name = "phylo")
tree_name
Deprecated. Use tree.name instead.
relabel.tree
Logical scalar. Should the tip labels be relabeled using
the output of getTaxonomyLabels(x, with_rank = TRUE)?
(Default: FALSE)
relabel_tree
Deprecated. Use relavel.tree instead.
order.tree
Logical scalar. Should the tree be ordered based on
alphabetic order of taxonomic levels? (Default: FALSE)
order_tree
Deprecated. Use order.tree instead.
levels.rm
Logical scalar. Should taxonomic level information
be removed from labels? (Default: FALSE)
remove_levels
Deprecated. Use levels.rm instead.
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)
show_label, show_highlights, show_highlight_label, abbr_label
Deprecated.
Use show.label, show.highlights, show.highlight.label, abbr_label instead.
add.legend
Logical scalar. Should legends be plotted?
(Default: TRUE)
add_legend
Deprecated. Use add.legend instead.
layout
layout for the plotted tree. See
ggtree for details.
edge.colour.by
Character scalar. Specification of a column metadata field or a feature
to colour tree edges by, see the by argument in
?retrieveCellInfo for possible
values.
edge_colour_by
Deprecated. Use edge.colour.by instead.
edge.size.by
Character scalar. Specification of a column metadata field or a feature
to size tree edges by, see the by argument in
?retrieveCellInfo for possible
values. (Default: NULL)
edge_size_by
Deprecated. Use edge.size.by instead.
tip.colour.by
Character scalar. Specification of a column metadata field or a feature to
colour tree tips by, see the by argument in
?retrieveCellInfo for possible
values. (Default: NULL)
tip_colour_by
Deprecated. Use tip.colour.by instead.
tip.shape.by
Character scalar. Specification of a column metadata field or a feature to
shape tree tips by, see the by argument in
?retrieveCellInfo for possible
values. (Default: NULL)
tip_shape_by
Deprecated. Use tip.shape.by isntead.
tip.size.by
Character scalar. Specification of a column metadata field or a feature to
size tree tips by, see the by argument in
?retrieveCellInfo for possible
values. (Default: NULL)
tip_size_by
Deprecated. Use tip.size.by instead.
node.colour.by
Character scalar. Specification of a column metadata field or a feature to
colour tree nodes by. Must be a field from other.fields. (Default: NULL)
node_colour_by
Deprecated. Use node.colour.by instead.
node.shape.by
Character scalar. Specification of a column metadata field or a feature to
shape tree nodes by. Must be a field from other.fields. (Default: NULL)
node_shape_by
Deprecated. Use node.shape.by instead.
node.size.by
Character scalar. Specification of a column metadata field or a feature to
size tree nodes by. Must be a field from other.fields. (Default: NULL)
node_size_by
Deprecated. Use node.size.by instead.
colour.highlights.by
Logical scalar. Should the highlights be colour differently?
If show.highlights = TRUE, colour_highlights will be set to
TRUE as default. (Default: FALSE)
colour_highlights_by
Deprecated. Use colour.highlights.by instead.
assay.type
Character scalar. or integer scalar. Specifies which assay to
obtain expression values from, for use in point aesthetics - see the
exprs_values argument in ?retrieveCellInfo.
(Default: "counts")
by_exprs_values
Deprecated. Use assay.type instead.
other.fields
Character vector. Additional fields to include in the node information
without plotting them. (Default: list())
other_fields
Deprecated. Use other.fields instead.
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
agglomerateByRanks
Examples
library(scater)
library(mia)
# preparation of some data
data(GlobalPatterns)
GlobalPatterns <- agglomerateByRanks(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 <- getTop(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 <- getTop(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 Aug. 13, 2024, 8:57 p.m.
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| plotTree | R Documentation |
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(x, ...)
plotColTree(x, ...)
## S4 method for signature 'TreeSummarizedExperiment'
plotColTree(
x,
tree.name = tree_name,
tree_name = "phylo",
relabel.tree = relabel_tree,
relabel_tree = FALSE,
order.tree = order_tree,
order_tree = FALSE,
levels.rm = remove_levels,
remove_levels = FALSE,
show.label = show_label,
show_label = FALSE,
show.highlights = show_highlights,
show_highlights = FALSE,
show.highlight.label = show_highlight_label,
show_highlight_label = FALSE,
abbr.label = abbr_label,
abbr_label = FALSE,
add.legend = add_legend,
add_legend = TRUE,
layout = "circular",
edge.colour.by = edge.colour.by,
edge_colour_by = NULL,
edge.size.by = edge_size_by,
edge_size_by = NULL,
tip.colour.by = tip_colour_by,
tip_colour_by = NULL,
tip.shape.by = tip_shape_by,
tip_shape_by = NULL,
tip.size.by = tip_size_by,
tip_size_by = NULL,
node.colour.by = node_colour_by,
node_colour_by = NULL,
node.shape.by = node_shape_by,
node_shape_by = NULL,
node.size.by = node_size_by,
node_size_by = NULL,
colour.highlights.by = colour_highlights_by,
colour_highlights_by = NULL,
assay.type = by_exprs_values,
by_exprs_values = "counts",
other.fields = other_fields,
other_fields = list(),
...
)
## S4 method for signature 'TreeSummarizedExperiment'
plotRowTree(
x,
tree.name = tree_name,
tree_name = "phylo",
relabel.tree = relabel_tree,
relabel_tree = FALSE,
order.tree = order_tree,
order_tree = FALSE,
levels.rm = remove_levels,
remove_levels = FALSE,
show.label = show_label,
show_label = FALSE,
show.highlights = show_highlights,
show_highlights = FALSE,
show.highlight.label = show_highlight_label,
show_highlight_label = FALSE,
abbr.label = abbr_label,
abbr_label = FALSE,
add.legend = add_legend,
add_legend = TRUE,
layout = "circular",
edge.colour.by = edge_colour_by,
edge_colour_by = NULL,
edge.size.by = edge_size_by,
edge_size_by = NULL,
tip.colour.by = tip_colour_by,
tip_colour_by = NULL,
tip.shape.by = tip_shape_by,
tip_shape_by = NULL,
tip.size.by = tip_size_by,
tip_size_by = NULL,
node.colour.by = node_colour_by,
node_colour_by = NULL,
node.shape.by = node_shape_by,
node_shape_by = NULL,
node.size.by = node_size_by,
node_size_by = NULL,
colour.highlights.by = colour_highlights_by,
colour_highlights_by = NULL,
assay.type = by_exprs_values,
by_exprs_values = "counts",
other.fields = other_fields,
other_fields = list(),
...
)
Arguments
x |
a
|
... |
additional arguments for plotting. See
|
tree.name |
|
tree_name |
Deprecated. Use |
relabel.tree |
|
relabel_tree |
Deprecated. Use |
order.tree |
|
order_tree |
Deprecated. Use |
levels.rm |
|
remove_levels |
Deprecated. Use |
show.label, show.highlights, show.highlight.label, abbr.label |
|
show_label, show_highlights, show_highlight_label, abbr_label |
Deprecated.
Use |
add.legend |
|
add_legend |
Deprecated. Use |
layout |
layout for the plotted tree. See
|
edge.colour.by |
|
edge_colour_by |
Deprecated. Use |
edge.size.by |
|
edge_size_by |
Deprecated. Use |
tip.colour.by |
|
tip_colour_by |
Deprecated. Use |
tip.shape.by |
|
tip_shape_by |
Deprecated. Use |
tip.size.by |
|
tip_size_by |
Deprecated. Use |
node.colour.by |
|
node_colour_by |
Deprecated. Use |
node.shape.by |
|
node_shape_by |
Deprecated. Use |
node.size.by |
|
node_size_by |
Deprecated. Use |
colour.highlights.by |
|
colour_highlights_by |
Deprecated. Use |
assay.type |
|
by_exprs_values |
Deprecated. Use |
other.fields |
|
other_fields |
Deprecated. Use |
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
agglomerateByRanks
Examples
library(scater)
library(mia)
# preparation of some data
data(GlobalPatterns)
GlobalPatterns <- agglomerateByRanks(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 <- getTop(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 <- getTop(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")
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