I'm using Cytoscape for generating a regulatory network. Are there any option for using multiple variables to set node size?
For example:
I have two groups A and B. The node size of the group be should be defined by the column 'expression' and the node size of the edgecount.
I try to select only the A nodes and set the node size by expression in styles but it change all the data set.
There isn't an easy way to do this in Cytoscape, but I'm not sure I understand what you're trying to achieve. You could create a combination column, but generally using size for two different variables is likely to confuse the viewers. I would suggest
Related
I'm have a large network of ~300K nodes that my machine has a hard time plotting with Cytpscape (Desktop version under Windows).
I know that the network has discrete groups that are not interconnected - I also have the id of those groups as a node attribute.
I want to be able to graph each group based on what id I select.
I tried achieving this with the filter (Cytoscape gave me the option to not plot the graph when opening it the first time - "Do you want to create a view for your large network now?") but it still seems to try to plot the entire graph when setting the filter and then clicking on "Create View".
So in short: Is there any way to "pre-filter" the graph, or to somehow else cut it up so that cytoscape will plot the one I want?
Any thoughts would be appreciated.
You are almost there. Once you have the filter set, then you need to create a subnetwork (see File > New Network), then you can create a view of that subset (or it will automatically be created if the node count is below the threshold).
In modeling, instances of the same label, i.e Student, have same set of properties. However, is it normal that instances of the same label have different sets of properties. For example, I have Product node:
(p:Product)-[:HAS_ATTRIBUTE]->(a:Attributes)
Different instances of Product result in different instances of Attributes. In this case, different Attributes nodes have very different properties.
Is this modeling normal? Different categories of products can have very different attributes.
It's very useful to have different properties. For instance, I have a Y-DNA project with single nucleotide polymorphisms (SNP) Nodes. Some are on the know haplotree and some are not. So, I set a property InHGTree to Y or blank to reflect this. Now I can more readily create queries using the haplotree branching.
BTW, relationships can also have different properties with the same value. DNA results from an individual are in a "kit." The kit is related to numerous SNPs. You want to be able to determine whether the kit is positive or negative for the SNP. It is most logically to put this fact in the relationship between the kit and the SNP.
It's certainly allowed, as there is no table schema as in relational dbs to enforce homogenous properties.
While this provides great flexibility, it may introduce complexity. It's up to the modelers and administrators of the database to provide any guidelines or implement restrictions, if needed.
While that would usually be in the form of convention, APOC triggers (or kernel extensions if you want to implement this yourself) could be used to enforce only certain properties for a node of a given label.
I have imported a csv file into neo4j. I have been trying to define a large number of properties (all the columns) for each node. How can i do that without having to type in each name?
I have been trying this:
USING PERIODIC COMMIT
load csv WITH headers from "file:///frozen_catalog.csv" AS line
//Creating nodes for each product id with its properties
CREATE (product:product{id : line.`o_prd`,
Gross_Price_Average: TOINT(line.`Gross_Price_Average`),
O_PRD_SPG: TOINT(line.`O_PRD_SPG`)});
You can adding properties from maps. For example:
LOAD CSV WITH HEADERS FROM "http://data.neo4j.com/northwind/products.csv" AS row
MERGE (P:Product {productID: row.productID})
SET P += row
http://neo4j.com/docs/developer-manual/current/cypher/clauses/set/#set-adding-properties-from-maps
The LOAD CSV command cannot perform automatic type conversion to ints on certain fields, that must be done explicitly (though you can avoid having to explicitly mention all other fields by using the map projection feature to transform your line data before setting it via stdob--'s suggestion).
You may want to take a look at Neo4j's import tool, as this will allow you to specify field type in headers, which should perform type conversion for you.
That said, 77 columns is a lot of data to all store on individual nodes. You may want to take another look at your data and figure out if some of those properties would be better modeled as nodes with their own label with relationships to your product nodes. You mentioned some of these were categorical properties. Categories are well suited to be modeled separately as nodes instead of as properties, and maybe some of your other properties would work better as nodes as well.
I am trying to use Gephi to help graph interview analysis results. The relationship map is only used to describe conventional connections and life cycles. What I would like to do is to size the nodes based on the number of interview responses that talk about the node, not the number of connections it has or the weighting of those connections. Can Gephi do this and if so, how do I do it please?
I have loaded in node weightings and can see this as part of node labels, but haven't been able to find a way of this having an effect on node size.
Many thanks
Data input field - change input format to integer
You can load the graph in gexf format adding a float attribute and add this attribute to ALL the nodes. It would like something like:
```
...
...
```
Once imported in Gephi, just go to the appearance tab and it will appear as one more attribute in "ranking" drop-down list.
If any problem with gefx format, let me know and I'll will share a whole example (just trying to remain short :-)
Regards
I want to add cases from many SPSS dataset to one SPSS dataset.
Here's my code:
DATASET ACTIVATE DataSet1.
ADD FILES /FILE=*
/FILE='Path\to\dataset.sav'.
EXECUTE.
But I get this error: Mismatched variable types on the input files.
I want SPSS to ignore the conflicting columns and add cases only from the columns where there is no conflict.
How do I do this?
This occurs because variables of the same name in the two different data sources have either different format types (STRING, NUMERIC, DATE ect) or either they are both STRINGS but of different length.
The latter, string variables of different lenghts, can be solved like this:
DATA LIST FREE / V(A1).
BEGIN DATA.
a b c
END DATA.
DATASET NAME DS1.
DATA LIST FREE / V(A2).
BEGIN DATA.
1 2 3
END DATA.
DATASET NAME DS2.
STATS ADJUST WIDTHS VARIABLES=ALL WIDTH=MAX /FILES DS1 DS2.
DATASET ACTIVATE DS1.
ADD FILES FILE=* /FILE=DS2.
However, if you have mismatch of different format types then that is a tad more complicated to solve due to many different permutations, so you would probably want to asses which variables are problematic and harmonize/delete them before merging files. Probably worth carrying out this exercise nonetheless as having same variable names with different format type could be signs of erroneous data.
If you know which variables conflict, you can use the KEEP subcommand to select the others, or you can use the RENAME command to assign new names and adjust the results afterwards.
If you need to harmonize the names and the issue is something like differing string lengths for variables that should be the same, the STATS ADJUST WIDTHS extension command can harmonize the widths before you merge.