plotGraph {miaViz} | R Documentation |
SummarizedExperiment
plotGraph
plots an igraph
object with additional information
matched from a SummarizedExperiment
object for the nodes only.
Information on the edges have to provided manually.
plotColGraph(x, y, ...) plotRowGraph(x, y, ...) ## S4 method for signature 'ANY,SummarizedExperiment' plotColGraph( x, y, show_label = FALSE, add_legend = TRUE, layout = "kk", edge_type = c("fan", "link", "arc", "parallel"), edge_colour_by = NULL, edge_width_by = NULL, colour_by = NULL, shape_by = NULL, size_by = NULL, by_exprs_values = "counts", other_fields = list(), ... ) ## S4 method for signature 'SummarizedExperiment,missing' plotColGraph(x, y, name = "graph", ...) ## S4 method for signature 'ANY,SummarizedExperiment' plotRowGraph( x, y, show_label = FALSE, add_legend = TRUE, layout = "kk", edge_type = c("fan", "link", "arc", "parallel"), edge_colour_by = NULL, edge_width_by = NULL, colour_by = NULL, shape_by = NULL, size_by = NULL, by_exprs_values = "counts", other_fields = list(), ... ) ## S4 method for signature 'SummarizedExperiment,missing' plotRowGraph(x, y, name = "graph", ...)
x, y |
a graph object and a
|
... |
additional arguments for plotting. See
|
show_label |
|
add_legend |
logical scalar. Should legends be plotted?
(default: |
layout |
layout for the plotted graph. See
|
edge_type |
type of edge plotted on the graph. See
|
edge_colour_by |
Specification of a edge metadata field to use for setting colours of the edges. |
edge_width_by |
Specification of a edge metadata field to use for setting width of the edges. |
colour_by |
Specification of a column metadata field or a feature to
colour graph nodes by, see the by argument in
|
shape_by |
Specification of a column metadata field or a feature to
shape graph nodes by, see the by argument in
|
size_by |
Specification of a column metadata field or a feature to
size graph nodes by, see the by argument in
|
by_exprs_values |
A string or integer scalar specifying which assay to
obtain expression values from, for use in point aesthetics - see the
|
other_fields |
Additional fields to include in the node information without plotting them. |
name |
If |
:
Internally tidygraph
and ggraph
are used. Therefore, all
graph types which can be converted by tidygraph::as_tbl_graph
can
be used.
a ggtree
plot
# data setup library(mia) data(GlobalPatterns) data(col_graph) data(row_graph) data(row_graph_order) metadata(GlobalPatterns)$col_graph <- col_graph genus <- agglomerateByRank(GlobalPatterns,"Genus",na.rm=TRUE) metadata(genus)$row_graph <- row_graph order <- agglomerateByRank(genus,"Order",na.rm=TRUE) metadata(order)$row_graph <- row_graph_order # plot a graph independently plotColGraph(col_graph, genus, colour_by = "SampleType", edge_colour_by = "weight", edge_width_by = "weight", show_label = TRUE) # plot the graph stored in the object plotColGraph(genus, name = "col_graph", colour_by = "SampleType", edge_colour_by = "weight", edge_width_by = "weight") # plot a graph independently plotRowGraph(row_graph, genus, colour_by = "Kingdom", edge_colour_by = "weight", edge_width_by = "weight") # plot the graph stored in the object plotRowGraph(genus, name = "row_graph", colour_by = "Phylum", edge_colour_by = "weight", edge_width_by = "weight") # plot a graph independently plotRowGraph(row_graph_order, order, colour_by = "Kingdom", edge_colour_by = "weight", edge_width_by = "weight") # plot the graph stored in the object and include some labels plotRowGraph(order, name = "row_graph", colour_by = "Phylum", edge_colour_by = "weight", edge_width_by = "weight", show_label = c("Sulfolobales","Spirochaetales", "Verrucomicrobiales")) # labls can also be included via selecting specific rownames of x/y plotRowGraph(order, name = "row_graph", colour_by = "Phylum", edge_colour_by = "weight", edge_width_by = "weight", show_label = c(1,10,50)) # labls can also be included via a logical vector, which has the same length # as nodes are present label_select <- rep(FALSE,nrow(order)) label_select[c(1,10,50)] <- TRUE plotRowGraph(order, name = "row_graph", colour_by = "Phylum", edge_colour_by = "weight", edge_width_by = "weight", show_label = label_select)