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Gephi Cheat Sheet (DRAFT) by

A cheat sheet to help navigate Gephi and address some common issues.

This is a draft cheat sheet. It is a work in progress and is not finished yet.

Graph area

Toolbars surrou­nding the graph on the left and bottom.
Open Additional settings via a button on the bottom right

Basic navigation

Zoom
Mouse wheel
Span
Right mouse drag

Basic selection and dragging

One node
Pressing down CTRL
X amount of nodes
Use "­Direct select­ion­" tool and use "­Con­fig­ure­"
Highlight area of interest
"­Direct select­ion­" tool
Drag nodes
"­Dra­g" tool

Appearance box

Top left. Most appearance related settings also use Additional settings from below the graph

Colors

Background
Additional settings -> Global -> Background color ✓
Nodes
Appearance -> Nodes (Color) -> Unique­/Pa­rti­tio­n/R­anking -> Apply
Edges
Default: edge color = node color. Otherwise: Appearance -> Edges (Color) -> Unique­/Pa­rti­tio­n/R­anking -> Apply
Labels
Additional settings -> Labels -> Node ✓
Label color = node color
Additional settings -> Labels -> Node ✓. Color -> Object

Sizes

Nodes
Appearance -> Nodes (Size) -> Unique­/Ra­nking -> Apply. If an attribute is added to the data, change the column values to "­flo­at" so it would pop up in Ranking options
Edges
Default: size depends on weight. Otherwise: Additional settings -> Edges -> Scale
Labels
Additional settings -> Labels -> Node ✓. Size -> Fixed/­Sca­led­/Node size
 

Layout box

Bottom left

Layout

Force Atlas
Small world/­scale free networks
Force Atlas 2
Updated Force Atlas, handles large data sets better, keeps high quality
Frucht­erm­an-­Rei­ngold
Simulates graph as system of mass particles. The algorithms aim to minimize the energy in the system. Standard but slow
Yifan Hu
Reduces comple­xity, fast, handles big data sets
OpenOrd
Expects undirected weighted graphs, aims to detect clusters. Really helpful on large graphs
GeoLayout
Based on latitu­de/­lon­gitude positions nodes, Mercarator projection linked to GMaps, coordi­nates should be numeric
Possible to write own algorithms and install other plugins online

Layout overlaps and geometric changes

Noverlap
Reduce Speed to increase quality, increase Margin and Ratio to increase space around nodes
Label adjust
Specific to visible labels.
Clockwise Rotate
Rotate -> Angle > 0
Counte­r-C­loc­kwise Rotate
Rotate -> Angle < 0
Expansion
Expand whole graph by scale vector
Contra­ction
Contract whole graph by scale vector
 

Filters | Statistics

Upper left

Statistics

Node size/color based on statistics
Statistics -> Run a selected statistic, the values will appear as options under node size and color in Appearance
Commun­ity­-de­tection
Statistics -> Modularity -> Run. Appearance -> Nodes (Color) -> Partition -> Modularity class

Filter

Remove nodes with a single edge
Filters -> Topology -> Degree range. To activate: Queries -> Degree range -> Move slider bound to 2 -> Filter

Viewing and exporting

Graph settings and Preview settings

Viewing

Graph
Window -> Graph
Data table
Window -> Data table
Timeline
Window -> Timeline
These are fixes in case the buttons "­Ove­rvi­ew", "Data Labora­tor­y", and "­Pre­vie­w" in the top left don't work

Preview and export

View preview
Window -> Preview. Window -> Preview settings -> Refresh
Large graph
Preview settings -> toggle Preview ratio bar
Curved edges
Preview settings -> Edges -> Curved ✓
Record snapshot
Graph visual­iza­tions bar, camera icon (Take screen­shot). Configure to change resolution
Export
Preview settings -> Export (SVG/P­DF/PNG)