Transcript Slide 1

EGAN Tutorial:
Interface Basics
October, 2009
Jesse Paquette
UCSF Helen Diller Family
Comprehensive Cancer Center
[email protected]
Preamble
• This document has many slides with multi-step
animations
– Best viewed in Slide Show mode
• The EGAN graphical user interface is evolving
– Icons may change
– Menus may change
– Button/widget placement may change
– This document probably won’t change as quickly
– Please contact the developers if you notice major
discrepancies between this and EGAN
Interface basics: Overview
• This document will introduce features and
components in EGAN in very simple and
general terms
• Launch the EGAN Demo to follow along
Interface basics: Overview
Welcome to EGAN!
Here’s the EGAN interface.
There’s a lot of information, so the
first thing you’ll want to master is
the ability to hide the parts you
don’t want to see.
Interface basics: Overview
The Network View
The Node Table
The EGAN interface can be divided
into three major components.
The Bottom Tables
Interface basics: Overview
There is a divider between the Network View
and the Node Table. You can drag this divider
If you
completely
Network
right
and wan
left totoprovide
moremaximize
room for the
either
There’s
also a divider
clickView
the Maximize
button.
theView,
Network
or the Node
Table,
between the upper section of
respectively.
theThere’s
interface
and the
a button
to Bottom
hide
Tables.
You
canTable.
drag this
just the
Node
divider up and down.
And a button to hide just the
Bottom Tables.
Interface basics: The Bottom Tables
When you have experiment results loaded,
there are four tables available. To show a
on to the Bottom
table,Let’s
clickmove
the corresponding
tab.Tables.
Interface basics: The Node Types Table
Right now the
Entrez Gene row is
firstnodes
table tab is the Node Types
selected.
Now all The
KEGG
Table.
This
table lists all the possible
Therefore
all
Entrez
are visible
in the
Node
node are
types that can be shown in the
Gene
Table. nodes
Table above. Select the KEGG row in
listed inNode
the Node
the Node Types Table.
Table.
Interface basics: The Edge Types Table
These rows cannot be selected
Node
Types Table.
Click the Edges like
tab in
to the
swap
to the
However, take note of the
Edge Types Table.
checkboxes in the first column.
Now the table displays all the types of
When
you click
one of these
gene-gene edges
currently
available
checkboxes, the corresponding
in EGAN.
edge type will be disabled in
EGAN. When disabled, edges
of this type will not be shown in
the Network View or used for
enrichment calculations.
Interface basics: The Experiments Table
Click the Expts. tab to swap to the
Experiments Table.
Now the table displays all experiment
results that have been loaded in
EGAN.
These checkboxes will allow you to show/hide some
of the experiment columns in the Node Table.
Interface basics: The Heatmap Table
The Heatmap Table is currently under
development. When genes are
shown in the Network View, they will
also be present here as rows in the
Heatmap Table.
Interface basics: The Node Table
Let’s move on to the
Node Table. Show the
Entrez Gene Node
Table by clicking the
Entrez Gene row in the
Node Types Table.
Interface basics: The Node Table
Let’s maximize our
view of the Entrez
Gene Node Table by
dragging the divider to
the left.
Interface basics: The Node Table
Now examine the rows and columns in the
Node Table. Each row displays information
corresponding to an Entrez Gene ID.
There are columns that list pre-collated
information about each gene, and columns
that display information about that gene in
the context of your experiments.
Interface basics: The Node Table
A useful feature of the Node Table is the
ability to sort the gene rows by one or more
columns.
Click on the p-value Affymetrix column
header. The first click will sort the rows in
ascending order, a second will sort the
rows in descending order. Make sure the
rows are sorted in ascending order.
Interface basics: The Node Table
Let’s select all genes that have Affymetrix
p-values of 0.0. We’re going to show
them on the Network View.
Click on the top gene row (ZKSCAN3) and
drag downwards until you have selected
all genes with Affymetrix p-values of 0.0.
Interface basics: The Node Table
You should have selected 68 genes. How
can you know how many genes are
selected?
Take
a look
down
in thethese
Nodenodes
Now
we’re
going
to show
Types Table.
Selected
in theThe
Network
View.Nodes
Drag column
the divider
should show
there
Entrez
back that
to the
rightare
so68
you
can see the
Gene nodes
selected.
Network
View. You can also click the
Hide node table button above the Node
Table.
Interface basics: The Network View
Click the Show selected button to
show all selected nodes.
Interface basics: The Network View
Now all 68 selected genes are shown in the
Network View…but they’re all located in the
same spot! To lay them out automatically, use
the Force layout button at the top of the Network
View.
Interface basics: The Network View
Ok, we’re almost done with
this tutorial. Just a few quick
pointers about using the
Network View.
Interface basics: The Network View
• You can Zoom in and out
– Use the buttons at the top of the Network View
– You can also use the mouse wheel to zoom
• You can pan around
– Click the right mouse button in empty network space and
drag in the direction you want to pan the view
– Similar to Google Maps
• You can select nodes by left-click
– Holding down the Shift key will toggle node selection
– You can group-select nodes
• Click the left mouse button in empty network space and drag the
red rectangle to define the nodes to select
• A left-click in empty network space will de-select all nodes
• You can move nodes around manually
– Left click-and-drag
– All selected nodes will be moved concurrently
Interface basics: A few tips
• There are lots of helpful buttons and rightclick pop-up menus
– If you hover the mouse over a button, a tooltip
will describe what the button will do
– Try right-clicking on rows in the Node
Table/Bottom Tables and also on nodes and
edges in the Network View.
• Don’t panic!
– There’s a lot of functionality in EGAN
Questions/comments?
• Visit http://groups.google.com/group/ucsf-egan
for downloads, documentation and discussion
– Requires an account with Google Groups