Network Visualization

_images/network.png

Style

EnrichmentMap creates a separate visual style for each network. The visual style has the following characteristics:

  • Nodes represent gene sets.
  • Node size represents the number of genes in the gene set.
  • Edges represent overlap (similarity) between gene sets.
  • Edge width represents the number of genes that overlap between a pair of gene sets.
  • Node fill represents enrichment scores, such as NES (for GSEA), p-value or q-value.
    • When there is only 1 data set the enriched phenotype is conveyed using a color gradient.
    • When there are 2 or more data sets nodes are overlayed with charts, where each segment of the chart shows enrichment using a color gradient.

The network is arranged by a force directed layout which causes gene sets with high overlap to cluster together.

Expression data is visualized in a separate panel called the Heat Map panel. For more details see Expression Panel (Heat Map).

Visual Properties

Warning

EnrichmentMap automatically maintains the visual properties described below. If you manually change these visual properties EnrichmentMap will overwrite your changes. If you want to create a custom visual style you must first create a copy and then make changes to the copy.

Visual properties are available on the Style tab of the Control Panel.

_images/style_tab.png

Node Visual Properties

There are two types of nodes:

  1. Enrichment gene set nodes
    • Regular gene set nodes that are created when the network is first created.
    • Enrichment nodes can have many different visualizations depending on the settings in the Style section of the Main Panel.
  2. Signature gene set nodes
    • Added to an existing network by Post Analysis.
    • Do not have chart visualizations.
    • Edges connected to signature nodes are dashed.
Enrichment Signature
node_enr node_sig

Visual properties

Visual Property Meaning Type Column(s)
Shape Gene Set Type Discrete Mapping EM#_GS_Type (ENR = Square, SIG = Diamond)
Fill Color NES, p/q-value Discrete Mapping EM#_pvalue, EM#_fdr_qvalue, EM_NES
Label Gene set name Passthrough Mapping EM#_GS_DESCR
Size Size of gene set Continuous Mapping EM#_gs_size
Image/Chart 1 NES, p/q-value Chart EM#_pvalue, EM#_fdr_qvalue, EM_NES

Edge Visual Properties

If there are 2 data sets, and/or the Separate edge for each data set option was chosen, then edges will have different colors for each data set. The edge color corresponds to the color of the icon next to the data set name in the main panel.

_images/separate_edges.png

If the network has only one data set, or if the Combine edges across data sets option was chosen, then all the edges between enrichment gene sets will be the same color.

_images/combined_edges.png

Edges connected to signature gene sets have a different color and are dashed.

_images/signature_edges.png

Visual properties

Visual Property Meaning Type Column(s)
Line Type Edge Type Discrete Mapping interaction (default = solid, sig = dashed)
Stroke Color Data Set or Signature Discrete Mapping EM#_Data Set
Width Size of gene set overlap Continuous Mapping EM#_similarity_coefficient

Chart Visualization

There are 3 types of chart available for visualizing enrichment values.

Radial Heat Map Heat Map Heat Strips
chart1 chart2 chart3

Each segment of the chart is equal size and represents the enrichment value from one data set. The color of each chart segment is a color gradient indicating the enrichment value. The default color scheme shows down-regulated scores in red and up-regulated scores in blue.

The legend dialog can be used to see which chart segment corresponds to which data set and the color gradient.

_images/legend1.png

Use the Style section of the Main Panel to change the type chart and the color scheme.

_images/style_panel.png