network visualization by cytoscape tutorial based on group layout

[@asmaakamal9663]

Hi Lucy. Thank you so much for this amazing video . I have a problem , whenever I make adjustments in the excel file , they do not reflect in cytoscape , for example I write unclustered , it still appears empty at cytoscape so I can not group by cluster. Any thoughts ???

[@muhammadshoaib-c2w]

can you please help us to calculate OTU abundance with tutorial video.

[@honeydzikrimarhaeny9629]

Why dont you show us how to prepare the nodes.txt file that contain mean abundance? It will make your tutorial clearly for the beginner.

[@Cleitonklt]

The considered correlation value is above 0.5? I tried to my all data set and no group are formed.

[@lucyzhang9850]

the group layout is based on phylum

[@languagetalk8141]

Hi, how could we make a network from a matrix: first column: name of genes and First row also name of the genes. The values are numeric ida

[@lucyzhang9850]

I use R script to run correlation analysis and also add attribute column. I have not tried to import matrix. You may try conet plugin.

[@lucyzhang9850]

yes, you can import numeric matrix to cytoscape. but I like to melt the data to long shape, change it to source and target column.

[@qndnada5249]

Hai ...how did you make the abundance table

[@lucyzhang9850]

using dplyr to calculate the mean or other attribute

[@johirislam8174]

Hi,I want to visualize my PPI network into cytoscape.But my ppI node are 661 and edges are 680 and seeds are 15.So i feel problem of visualizing it into cytoscape.Because of huge number of nodes and edges. So how can i visualize this .I mean to say I want to know the way that can visualize all the interacted nodes clearly. Clearly means all the lebels are being clearly watched in manuscript.

[@lucyzhang9850]

you might use gephi to visualize the large datasets

[@johirislam8174]

@@lucyzhang9850 for use this software will java have to be installed into the PC?

[@lucyzhang9850]

@@johirislam8174 yes, to use gephi, you need install jre

[@johirislam8174]

@@lucyzhang9850 I opened it but i want to visualize my gene interaction network that i have analysed with network analyst platform .The fle fornat is .sif .So how can i open this file into gephi??

[@lucyzhang9850]

@@johirislam8174 normally, I export edge and node table out, and import

[@vitaltopics316]

How to get the abundance values for the nodes?

[@lucyzhang9850]

I use R to calculate mean abundance.

[@vitaltopics316]

@@lucyzhang9850 could you please give me the command? can I send you an email please?

[@lucyzhang9850]

@@vitaltopics316 I can sell you the script 10$ if you need.

[@namitapaudel3864]

@@vitaltopics316 If you have OTU table, you can calculate abundance manually in Excel

[@vitaltopics316]

@@namitapaudel3864 thank you, Namita

[@LnNJBFANZ]

thank you!

[@seheromezli9821]

hi, how did you open the excel file ? which program did you run? excel file not edited and it loks like text

[@lucyzhang9850]

save excel as tab delimited txt before import

[@lucyzhang9850]

just drag text file to excel sheet directly. excel can open text file with tab delimnated

[@seheromezli9821]

@@lucyzhang9850 thank you

[@ky_rien]

Oboblhohohohohlyo

[@ky_rien]

Boo

[@ahmedal-mammari9639]

plz do you have wechat ID

[@lucyzhang9850]

983499199