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Create enrichMap igraph object from enrichResult, deprecated

Source: R/jamenrich-base.r
enrichMapJam.Rd

Create enrichMap igraph object from enrichResult, deprecated, use mem2emap().

Usage

enrichMapJam(
  x,
  n = 50,
  vertex.label.font = 1,
  vertex.label.cex = 1,
  keyColname = "ID",
  nodeLabel = c("Name", "Description", "ID"),
  descriptionColname = "Description",
  nodeLabelFunc = NULL,
  overlapThreshold = 0.2,
  msigdbGmtT = NULL,
  verbose = FALSE,
  ...
)

Arguments

x

enrichResult or data.frame containing enrichment results, specifically expecting colnames to contain one of c("ID","Description","Name") to represent the node name, and c("Description") to represent the description, if present.

n

numeric value indicating the maximum number of nodes to include in the final network.

vertex.label.font, vertex.label.cex

numeric values to define the default node label font and size.

keyColname, nodeLabel, descriptionColname

character vectors indicating the colname to use for the node name and label.

nodeLabelFunc

function, default NULL uses fixSetLabels(x, width=30, ...). Use 'FALSE' to keep labels unchanged. Note that the igraph node name remains the same as input, and label is used as the visual label on the graph.

  • When providing a custom function, note that each node is called individually and therefore the call is not vectorized.

overlapThreshold

numeric value indicating the minimum Jaccard overlap, where edges with lower values are deleted from the igraph object.

msigdbGmtT

not currently implemented.

...

additional arguments are passed to enrichDF2enrichResult() when the input x is a data.frame.

Value

igraph object with nodes representing each pathway, sized based upon the number of genes involved in enrichment, and colored based upon the -log10(Pvalue) using colorjam::col_linear_xf(), a function that applies a color gradient to a numeric range. Each edge has attributes: overlap containing Jaccard overlap, overlap_count with the number of genes in common between the two nodes, and overlap_max_pct with the maximum percent overlap between two nodes (overlap count)/(smaller node size).

Details

This function is a minor customization to enrichplot::emapplot(), which takes a single enrichResult and produces an Enrichment map network. For the equivalent function using Mem as input, see mem2emap().

The major differences compared with enrichplot:

  • An igraph object is returned instead of ggplot object, since the igraph object can be manipulated and is useful to review.

  • This function calculates overlap using dist(...,method="binary") which is a much faster method for calculating the Jaccard overlap.

  • This function also calculates the overlap count, another helpful measure for filtering network connections, for example to remove links with only one gene, even if they overlap is above the required threshold. Many spurious network connections are removed with this filter, and it appears to be a helpful option.

See also

Other jam deprecated functions: cnetplotJam(), grid_with_title(), mem_multienrichplot(), with_qfr()