MultiEnrichMap plot
Usage
mem_multienrichplot(
mem,
overlap = 0.1,
overlap_count = 2,
do_plot = TRUE,
do_legend = TRUE,
remove_blanks = TRUE,
remove_singlets = TRUE,
spread_labels = TRUE,
y_bias = 1,
label_edges = c("overlap_count", "count", "overlap", "label", "none"),
edge_cex = 1,
node_cex = 0.8,
node_size = 5,
edge_color = "#55555588",
frame_color = "#55555500",
shape = "pie",
repulse = 3.7,
sets = NULL,
rescale = TRUE,
edge_bundling = "connections",
main = "MultiEnrichMap\noverlap >= {overlap}, overlap_count >= {overlap_count}",
...
)
Arguments
- mem
list
object output frommultiEnrichMap()
, specifically containing elements"multiEnrichMap","multiEnrichMap2"
which are expected to beigraph
objects.- overlap
numeric value between 0 and 1, indicating the Jaccard overlap filter to use for edge nodes. The value is used to delete edges whose values
E(g)$overlap
are below this threshold.- overlap_count
numeric value indicating the minimum overlap count below which edges are removed. The value
E(g)$overlap_count
is used for this filter.- do_plot
logical indicating whether to plot the final result.
- do_legend
logical indicating whether to print a color legend, valid when
do_plot=TRUE
. Arguments...
are also passed tomem_legend()
, for examplex="bottomleft"
can be overriden.- remove_blanks
logical indicating whether to call
removeIgraphBlanks()
which removes blank/empty colors in igraph nodes.- remove_singlets
logical indicating whether to remove singlet nodes, which are nodes that have no connections to other nodes. By default, singlets are removed, in order to help visualize the node connections that remain after filtering by
overlap
.- spread_labels
logical indicating whether to call
spread_igraph_labels()
, which places node labels at an angle offset from the node, in order to improve default label positions.- y_bias
numeric value passed to
spread_igraph_labels()
whenspread_labels=TRUE
.- repulse
numeric value used for network layout when
layout_with_qfrf()
is used.- sets
optional character vector of enriched sets to include, all other sets will be excluded. These values are matched with
V(g)$name
.- rescale
logical indicating whether the
igraph
layout coordinates are scaled to rangec(-1, 1)
before plotting. In practice, whenrescale=FALSE
the functionjam_igraph()
is called because it does much better at properly handling other settings during the change. The effect is mainly to keep layout aspect intact, in cases where the x- and y-axis ranges are not roughly the same size, for example a short-wide layout.- main
character string used as the title when
do_plot=TRUE
. This character string is passed toglue::glue()
in order to include certain argument values such asoverlap
.- ...
additional arguments are passed to
removeIgraphBlanks()
,removeIgraphSinglets()
, andspread_igraph_labels()
as needed.
Value
invisibly returns the igraph
object used for plotting,
a by-product of this function when do_plot=TRUE
is that
the igraph object is also visualized. All custom plot elements
are updated in the igraph
object, so in principle a
simple call to plot(...)
should suffice.
Details
This function is likely to be replaced by mem2emap()
.
This function takes output from multiEnrichMap()
and produces
customized "multiple enrichMap" plots using an igraph network.
It differs from the data provided from multiEnrichMap()
mostly
by enabling different overlap filters, and by automating
several steps that help with network layout, and node label
placement.
For the most flexible exploration of data, run multiEnrichMap()
using a lenient overlapThreshold
, for example overlapThreshold=0.1
.
Then call this function with increasing overlap
until the
visualization has insightful structure.
See also
Other jam igraph functions:
cnet2df()
,
cnet2im()
,
cnetplotJam()
,
cnetplot_internalJam()
,
color_edges_by_nodegroups()
,
color_edges_by_nodes()
,
color_edges_by_nodes_deprecated()
,
color_nodes_by_nodegroups()
,
communities2nodegroups()
,
drawEllipse()
,
edge_bundle_bipartite()
,
edge_bundle_nodegroups()
,
enrichMapJam()
,
fixSetLabels()
,
flip_edges()
,
get_bipartite_nodeset()
,
highlight_edges_by_node()
,
igraph2pieGraph()
,
jam_igraph()
,
jam_plot_igraph()
,
label_communities()
,
layout_with_qfr()
,
layout_with_qfrf()
,
mem2emap()
,
memIM2cnet()
,
nodegroups2communities()
,
rectifyPiegraph()
,
relayout_with_qfr()
,
removeIgraphBlanks()
,
removeIgraphSinglets()
,
reorderIgraphNodes()
,
rotate_igraph_layout()
,
spread_igraph_labels()
,
subgraph_jam()
,
subsetCnetIgraph()
,
subset_igraph_components()
,
sync_igraph_communities()
,
with_qfr()
Other jam plot functions:
adjust_polygon_border()
,
grid_with_title()
,
jam_igraph()
,
mem_enrichment_heatmap()
,
mem_gene_path_heatmap()
,
mem_legend()
,
mem_plot_folio()
,
plot_layout_scale()