memIM2cnet: Convert MultiEnrichment incidence matrix to Cnet plot

In jmw86069/multienrichjam: Analysis and Visualization of Multiple Gene Set Enrichments

Convert MultiEnrichment incidence matrix to Cnet plot

Description

Convert MultiEnrichment incidence matrix to Cnet plot

Usage

memIM2cnet(
  memIM,
  categoryShape = c("pie", "coloredrectangle", "circle", "ellipse"),
  geneShape = c("pie", "coloredrectangle", "circle", "ellipse"),
  categoryColor = "#E5C494",
  geneColor = "#B3B3B3",
  categoryLabelColor = "darkblue",
  geneLabelColor = "grey25",
  categorySize = 6,
  geneSize = 3,
  categoryCex = 0.8,
  geneCex = 0.5,
  frame_darkFactor = NULL,
  geneIM = NULL,
  geneIMcolors = NULL,
  geneIMdirection = NULL,
  enrichIM = NULL,
  enrichIMcolors = NULL,
  enrichIMdirection = NULL,
  coloredrect_nrow = 1,
  coloredrect_ncol = NULL,
  coloredrect_byrow = TRUE,
  colorV = NULL,
  direction_col = colorjam::col_div_xf(1.2),
  hide_solo_pie = TRUE,
  remove_blanks = TRUE,
  spread_labels = FALSE,
  repulse = 3.5,
  verbose = FALSE,
  ...
)

mem2cnet(
  memIM,
  categoryShape = c("pie", "coloredrectangle", "circle", "ellipse"),
  geneShape = c("pie", "coloredrectangle", "circle", "ellipse"),
  categoryColor = "#E5C494",
  geneColor = "#B3B3B3",
  categoryLabelColor = "darkblue",
  geneLabelColor = "grey25",
  categorySize = 6,
  geneSize = 3,
  categoryCex = 0.8,
  geneCex = 0.5,
  frame_darkFactor = NULL,
  geneIM = NULL,
  geneIMcolors = NULL,
  geneIMdirection = NULL,
  enrichIM = NULL,
  enrichIMcolors = NULL,
  enrichIMdirection = NULL,
  coloredrect_nrow = 1,
  coloredrect_ncol = NULL,
  coloredrect_byrow = TRUE,
  colorV = NULL,
  direction_col = colorjam::col_div_xf(1.2),
  hide_solo_pie = TRUE,
  remove_blanks = TRUE,
  spread_labels = FALSE,
  repulse = 3.5,
  verbose = FALSE,
  ...
)

Arguments

memIM	numeric matrix, or mem output in list format. When mem format is supplied, relevant arguments which are empty will use corresponding data from mem, for example geneIM, geneIMcolors, enrichIM, enrichIMcolors.
categoryShape, geneShape	character string indicating the preferred default node shape. In general, pie shapes with one segment are converted to circle for simplicity during plot functions, although when using jam_igraph() to plot, it will treat single-segment pie nodes as circle anyway, and vectorizes pie node plotting to make the overall rendering time substantially faster.
categoryColor, geneColor	character R color for default node colors, used when geneIMcolors,enrichIMcolors is not supplied, respectively.
categoryLabelColor, geneLabelColor	character R color used as default node label color.
categorySize, geneSize	numeric default node size.
categoryCex, geneCex	numeric adjustment to default node label font size.
frame_darkFactor	numeric passed to jamba::makeColorDarker() so the frame color is slightly darker than the node fill color.
geneIM, geneIMcolors, geneIMdirection, enrichIM, enrichIMcolors, enrichIMdirection	matrix objects typically associated with mem output from multiEnrichMap(), however they are optional so this function can be applied broadly to any incidence matrix. geneIMcolors is used to define gene (row) node colors enrichIMcolors is used to define set (column) node colors geneIMdirection,enrichIMdirection is used to define optional border colors defined by the direction, where -1 is down, 0 is no change, and +1 is up. Use direction_col to define a custom color function.
coloredrect_nrow, coloredrect_ncol, coloredrect_byrow	arguments used when geneShape="coloredrectangle", to define layout and placement of colors across columns in geneIMcolors. By default, one row of colors is used.
colorV	character optional vector of R colors, named by enrichment names that appear in colnames(enrichIM) when supplied. When defined, these colors override those defined in enrichIMcolors.
remove_blanks	logical indicating whether to remove blank subsections from each node, by calling removeIgraphBlanks().
spread_labels	logical indicating whether to call spread_igraph_labels() to orient labels radially away from incoming edges.
verbose	logical indicating whether to print verbose output.
...	additional arguments are passed to downstream functions: when remove_blanks=TRUE it is passed to removeIgraphBlanks() when spread_labels=TRUE it is passed to spread_igraph_labels()

Details

This function takes list output from multiEnrichMap() and uses three elements to create a Cnet plot:

1. "memIM" gene-pathway incidence matrix

2. "geneIM" the gene incidence matrix

3. "enrichIM" the pathway enrichment matrix

Value

igraph object with Concept network data, containing pathways connected to genes. Each node has attribute "nodeType" of either "Set" or "Gene".

See Also

Other jam igraph functions: cnet2df(), cnet2im(), cnetplotJam(), cnetplot_internalJam(), color_edges_by_nodegroups(), color_edges_by_nodes_deprecated(), color_edges_by_nodes(), color_nodes_by_nodegroups(), communities2nodegroups(), drawEllipse(), edge_bundle_bipartite(), edge_bundle_nodegroups(), enrichMapJam(), fixSetLabels(), flip_edges(), get_bipartite_nodeset(), igraph2pieGraph(), jam_igraph(), jam_plot_igraph(), label_communities(), layout_with_qfrf(), layout_with_qfr(), mem2emap(), mem_multienrichplot(), 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()

jmw86069/multienrichjam documentation built on Nov. 3, 2024, 10:29 p.m.