memIM2cnet: Convert MultiEnrichment incidence matrix to Cnet plot
In jmw86069/jamenrich: Analysis and Visualization of Multiple Gene Set Enrichments

memIM2cnet

R Documentation

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:

"memIM" gene-pathway incidence matrix
"geneIM" the gene incidence matrix
"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".

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()