Question: cytoscape: change shape of target
0
gravatar for simonjean434
4.5 years ago by
simonjean43450
simonjean43450 wrote:

Hello,

I loaded a network in cytoscape 3.4 and would like to change the shape of subset of nodes. I selected some nodes and changed the shape style but when I applied this modification the shape of all nodes in the network changed.

could you please help me with this ?

Thanks S

rna-seq • 2.7k views
ADD COMMENTlink modified 4.5 years ago by Jean-Karim Heriche24k • written 4.5 years ago by simonjean43450
1
gravatar for Jean-Karim Heriche
4.5 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche24k wrote:

You need to do this with discrete mapping to a node attribute (i.e. column of the node table). In the style control panel, click on the little triangle next to Shape to expand the selector, then select a column, select discrete mapping as mapping type then select a shape for each category of nodes.

ADD COMMENTlink written 4.5 years ago by Jean-Karim Heriche24k

sorry I exactly performed as you described but all of network changing when I am trying to change the shape of selected nodes. then what to do please?

ADD REPLYlink written 3.8 years ago by A3.9k
1

If you did as explained but all nodes are changing, it's likely because you have assigned the same attribute to all nodes. Create an attribute for the nodes that reflects the distinction you're trying to make between the nodes then apply the mapping using this attribute. If you already did so, then make sure that you've selected the right attribute when doing the shape mapping.

ADD REPLYlink written 3.8 years ago by Jean-Karim Heriche24k

thank you

my network is like below (33 nodes and 56 edges)

TF gene

AHR SGIP1

AHR CDC42

AP-2gamma CDC42

AP-2gamma LPPR4

AP-2gamma ARID1A

I imported txt file of network via import=network=file in Cytoscape 3.4.0. then in preview window I set TFs as source node and genes as target node. when network uploaded I selected TFs by select option=nodes=from ID list file. when TFs hilighted in network, in style in column i chose selected and in mapping type I set discrete mapping. but whole of network changed

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by A3.9k

You haven't done as described. You need to add an attribute that can be mapped to the shape. This can simply be a column called "shape" that, for each node, tells which shape it should be. You then apply the discrete mapping as already explained.

ADD REPLYlink written 3.7 years ago by Jean-Karim Heriche24k

enter image description here

sorry I can't find the shape column

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by A3.9k

It's your data. You decide which node should have which shape so you have to tell Cytoscape where this information is. You have to add it yourself.

ADD REPLYlink written 3.7 years ago by Jean-Karim Heriche24k

sorry, I want to re-shape TFs which I highlighted them in network by select option but I can't merely change them yet because I don't know how to tell Cytoscape to only change them. shape option in style seems deactivated

https://r76i.imgup.net/shapee838.png

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by A3.9k

Yes I understood your question but you don't seem to understand my answer. The answer is: add a column to your data node table with the information about node shape. The node table is in the table panel, which is the panel normally found below the graph drawing area.

ADD REPLYlink written 3.7 years ago by Jean-Karim Heriche24k

thank you, I added column, for node information I added a shape name (diamon) to entire the column but ..

I am sorry

https://e46i.imgup.net/shape44b6.png

ADD REPLYlink written 3.7 years ago by A3.9k

Very useful comment!! Thanks!

ADD REPLYlink written 2.4 years ago by cecilia.jimenez-sanchez0
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