Merging two PPIs with different colors
Jerry
I made two differnt PPIs. I picked color green for PPI(1)
and color blue for PPI(2). When I merged two PPIs, the color of
mereged PPI turn into PPI(2); however, I would like to keep different
colors for each PPI even after merging them. Any idea?
Thanks,
Jerry
scooter
What you need to do is to add an attribute to the nodes (and edges,
if desired) in each PPI (say "PPI Number"). Then you can use the
VizMapper to color the nodes based on the PPI Number the node came
from. Obviously, if you have nodes that are shared between the two
networks, then you will only get one color...
-- scooter
Jiao Li
Thanks,
Jiao
--
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
To post to this group, send email to cytoscape...@googlegroups.com.
To unsubscribe from this group, send email to cytoscape-helpd...@googlegroups.com.
For more options, visit this group at http://groups.google.com/group/cytoscape-helpdesk?hl=en.
Scooter Morris
Is there a way to make a node with more than one colors? In this case, a protein is involved in two networks.
Thanks,
Jiao
-- scooter
Jerry
May you clarify what you mean? "What you need to do is to add an
attribute to the nodes" .
Another question is when I merged two PPIs, the shape of merged PPI is
not a globe but it is a square. How may I turn it into a globe?
Thanks,
Jerry
karim mezhoud
Before mergin give a class for every network.
1-select all node label from PPI1.
2- copy your list name from the panel
3- past it in speedsheet
4- add une second column "="
5- add in the third column "green"
6- save as PPI1.NA
do the same this with your PPI2 but change the color.
13- import the PPI1.NA as node attributes
14-double click in node colore (VizMapper)
15- select "PPI1", "Discrete mapping", and select color.
do the same this with your PPI2 but change the color.
regards
kmezhoud
--
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
To post to this group, send email to cytoscape...@googlegroups.com.
To unsubscribe from this group, send email to cytoscape-helpd...@googlegroups.com.
For more options, visit this group at http://groups.google.com/group/cytoscape-helpdesk?hl=en.
Vijayaraj Nagarajan
The attached image with an example merged network might give you an idea about what Scooter was suggesting.
Take note of the "data panel" attribute names/values and the "vizmapper" coloring schemes.
Hope this helps.
Cheers,
Vijay
Jerry
PPI. I got what Vijay said, but I have problem with previuos steps.
Although, I tried to understand what Karim said, I still don't know
how to make two differnt nodes attributes for two PPIs at pannel.
Note that, I have already made two PPIs with more than 8000 nodes for
each PPI.
Thanks,
Jerry
> 320KViewDownload
mezhoud
build a file as in attach. In this file there are two classes PPI-I and
PPI-II.
If you have a commun nodes, you must create a third class for example
PPI-III
Import this file as node attributes.
activate node color
choose PPI-1+PPI-II
choose Discrete mapping
select colors
for the three classes.
Regards
karim
Le 21/05/2012 19:21, Jerry a �crit :
�__
Jerry
| P-I (class=java.lang.String) | ||
| ABC | = | P-I |
| ABCB | = | P-I |
| ABO | = | P-I |
| ABL | = | P-I |
| P-II (class=java.lang.String) | ||
| FUY | = | P-II |
| ABG | = | P-II |
| PKC | = | P-II |
| AKT3 | = | P-II |
| ID | P-I | P-II |
| 2541 | null | null |
| 3267 | null | null |
| 231 | null | null |
| 29874 | null | null |
On Tuesday, May 22, 2012 5:43:30 AM UTC-4, karim mezhoud wrote:
Hi,
build a file as in attach. In this file there are two classes PPI-I and
PPI-II.
If you have a commun nodes, you must create a third class for example
PPI-III
Import this file as node attributes.
activate node color
choose PPI-1+PPI-II
choose Discrete mapping
select colors
for the three classes.
Regards
karim
Le 21/05/2012 19:21, Jerry a �crit :
>>> To post to this group, send email to cytoscape-helpdesk@googlegroups.com.
>>> To unsubscribe from this group, send email to
>>> cytoscape-helpdesk+unsub...@googlegroups.com.
>>> For more options, visit this group at
>>> http://groups.google.com/group/cytoscape-helpdesk?hl=en.
>>
>>
>>
>> merge.png
>> 320KViewDownload
>
--
�__
c/ /'_;~~~~~~kmezhoud
(*) \(*)
http://bioinformatics.tn/
PPI-1+PPI-2 (class=java.lang.String)
SERPINA1 = PPI-I
ADAMTS13 = PPI-I
CRP = PPI-I
EFEMP1 = PPI-I
YWHAZ = PPI-I
IGKV2-30 = PPI-I
HPX = PPI-I
ADIPOQ = PPI-I
APOC3 = PPI-I
IGFBP5 = PPI-I
AFM = PPI-I
F2 = PPI-I
FN1 = PPI-I
F13B = PPI-I
C1QTNF3 = PPI-I
ENO1 = PPI-I
LV301 = PPI-I
SERPINA4 = PPI-I
SAA1 = PPI-I
PCOLCE = PPI-I
VWF = PPI-I
ITIH2 = PPI-I
C20ORF3 = PPI-I
HV305 = PPI-I
APOE = PPI-I
QPCT = PPI-I
GSN = PPI-I
LTF = PPI-I
TPM4 = PPI-I
MGP = PPI-I
ITIH4 = PPI-I
SAA4 = PPI-I
THBS1 = PPI-I
KRT1 = PPI-I
LV106 = PPI-I
IGF2 = PPI-I
AGT = PPI-I
CFHR4 = PPI-I
CDH1 = PPI-I
HIST1H2BD = PPI-I
NUCB1 = PPI-I
FGA = PPI-I
VCP = PPI-I
MASP2 = PPI-I
CP = PPI-I
PF4 = PPI-I
HBA1 = PPI-I
F12 = PPI-I
IGHG3 = PPI-I
DSG2 = PPI-I
PROC = PPI-I
HV320 = PPI-I
FBLN5 = PPI-I
CNDP1 = PPI-I
WISP2 = PPI-I
DEFA1 = PPI-I
PPBP = PPI-I
TTR = PPI-I
C1QB = PPI-I
OIT3 = PPI-I
C8B = PPI-I
FBN1 = PPI-I
APOA1 = PPI-I
MASP1 = PPI-I
RNASE4 = PPI-I
LYZ = PPI-I
CLEC3B = PPI-I
APCS = PPI-I
LCAT = PPI-I
HIST1H1D = PPI-I
CFH = PPI-I
PLG = PPI-I
HV207 = PPI-I
PON1 = PPI-I
F9 = PPI-I
APOL1 = PPI-I
C1S = PPI-I
IGFALS = PPI-I
CLU = PPI-I
P4HB = PPI-I
PLTP = PPI-I
SERPINA3 = PPI-I
CDH13 = PPI-I
CDH5 = PPI-I
IGKV3-11 = PPI-I
RARRES2 = PPI-I
F10 = PPI-I
PZP = PPI-I
C3 = PPI-I
GANAB = PPI-I
RBP4 = PPI-I
HABP2 = PPI-I
AMBP = PPI-I
C5 = PPI-I
SPTBN4 = PPI-I
HV201 = PPI-I
HGFAC = PPI-I
ORM1 = PPI-I
Breast_C = PPI-II
CRP = PPI-II
PPBP = PPI-II
LGALS3BP = PPI-II
TFRC = PPI-II
RBP4 = PPI-II
Lunch.Sq_C = PPI-II
ADH4 = PPI-II
CFHR2 = PPI-II
HBA1 = PPI-II
Glioblastoma_C = PPI-II
YWHAZ = PPI-II
TF = PPI-II
Prostate_C = PPI-II
Ovarian_C = PPI-II
COMP = PPI-II
Kidney_C = PPI-II
Colon_C = PPI-II
PRAP1 = PPI-II
CFHR1 = PPI-II
Jerry
Jerry
On Wednesday, May 16, 2012 7:45:58 AM UTC-4, Jerry wrote: