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Split brain networks - #125

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Islast wants to merge 47 commits into
WhitakerLab:masterfrom
Islast:splitBrainNetworks
Open

Split brain networks#125
Islast wants to merge 47 commits into
WhitakerLab:masterfrom
Islast:splitBrainNetworks

Conversation

@Islast

@IslastIslast commented Jul 4, 2019

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Collaborator
  • I'm ready to merge
    Not at all. This is just a preview of my proposed changes to seperate the BrainNetwork class into two distinct subclasses: BinaryBrainNetwork and WeightedBrainNetwork.

  • What's the context for this pull request?
    (this is a good place to reference any issues that this PR addresses)
    Ruslan discovered that when you run the threshold method on an already binarised graph it returns garbage.
    This made me think that there are potentially a lot of situations where treated a weighted network like a binary network or vice versa could be disastrous.

  • What's new?
    My thinking is that the difference between a weighted and a binarised brain network should be very explicit since it's going to determine what sort of analyses we can do on it.

It should be possible to threshold a WeightedBrainNetwork into a BinaryBrainNetwork and it should be possible to initialise a WeightedBrainNetwork from a correlation matrix.

A BinaryBrainNetwork should support all of the network analysis methods. We could run these on a weighted graph no problem, but they would tell us nothing about our data. We will record the original weightings on existent BinaryBrainNetworks in case we want to restrict our focus to fewer edges later (the specific use case being plotting).

  • What should a reviewer feedback on?
    Is this the right direction to go in to solve this problem.

  • Does anything need to be updated after merge?
    (e.g the wiki or the WhitakerLab website)

docs and tutorials would certainly need to be updated, but it's a little early for that.

Islastand others added 30 commits July 3, 2019 19:30
@Islast
Split BrainNetwork class into Weighted and Binary subclasses
ccd055e
@Islast
Merge branch 'paired-brains' of github.com:WhitakerLab/scona into pai…
42af7d1
…red-brains
@Islast
add split_groups function
5234b79
@Islast
add shuffleing to split_groups
fe91cfd
@KirstieJane
Add comments
309951a
@Islast
copy dataframe
360e7cf
@KirstieJane
Fix merge conflicts
e582376
Add comments, slightly restructure
@KirstieJane
First commit of tutorial to compare groups
4b1a44c
@KirstieJane
Add comments
3091d30
@Islast
implement patient grouping at correlation matrix level
8d72ba5
@Islast
unify parsers and install command line tools at setup
e54952b
@Islast
structure setup to install command line tools
960bc88
@Islast
unify parsers and install command line tools at setup
0cf0a26
@Islast
structure setup to install command line tools
1952f9e
@Islast
Merge branch 'commandline' of github.com:Islast/scona into commandline
7b4b8c5
@Islast
add split_groups function
d3f54eb
@Islast
add shuffleing to split_groups
640983d
@Islast
rebase onto master
8ddaaea
@KirstieJane@Islast
First commit of tutorial to compare groups
483c527
@Islast
implement patient grouping at correlation matrix level
e27bbf4
@Islast
better syntax for boolean evaluation
a731e9d
@Islast
Merge branch 'paired-brains' of github.com:Islast/scona into paired-b…
8385d93
…rains
@Islast
fix syntax error
92a392a
@Islast
Merge branch 'commandline' into paired-brains
a51eff3
@Islast
variable renaming
8b251ea
@Islast
replace scona.py wrapper
c2fb702
@Islast
writing out corrmat now optional
368c3df
@Islast
regression test command line tool
292f8b7
@Islast
add split_groups function
71ec9c9
@Islast
add shuffleing to split_groups
6ffcb6d
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2 participants

@Islast@KirstieJane
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Split brain networks by Islast · Pull Request #125 · WhitakerLab/scona · GitHub
Skip to content
Split brain networks - #125
Open
Islast wants to merge 47 commits into
WhitakerLab:masterfrom 
Islast:splitBrainNetworks
Open
Split brain networks#125
Islast wants to merge 47 commits into
WhitakerLab:masterfrom 
Islast:splitBrainNetworks
Conversation
@Islast
@IslastIslast
commented
Jul 4, 2019

Copy link


Copy Markdown

Collaborator
  •  I'm ready to merge
    
Not at all. This is just a preview of my proposed changes to seperate the BrainNetwork class into two distinct subclasses: BinaryBrainNetwork and WeightedBrainNetwork.
  • What's the context for this pull request?
    (this is a good place to reference any issues that this PR addresses)
    
Ruslan discovered that when you run the threshold method on an already binarised graph it returns garbage.
    
This made me think that there are potentially a lot of situations where treated a weighted network like a binary network or vice versa could be disastrous.
  • What's new?
    
My thinking is that the difference between a weighted and a binarised brain network should be very explicit since it's going to determine what sort of analyses we can do on it.
It should be possible to threshold a WeightedBrainNetwork into a BinaryBrainNetwork and it should be possible to initialise a WeightedBrainNetwork from a correlation matrix.
A BinaryBrainNetwork should support all of the network analysis methods. We could run these on a weighted graph no problem, but they would tell us nothing about our data. We will record the original weightings on existent BinaryBrainNetworks in case we want to restrict our focus to fewer edges later (the specific use case being plotting).
  • What should a reviewer feedback on?
    
Is this the right direction to go in to solve this problem.
  • Does anything need to be updated after merge?
    (e.g the wiki or the WhitakerLab website)
docs and tutorials would certainly need to be updated, but it's a little early for that.
Islastand others
added 30 commits
July 3, 2019 19:30
@Islast
Split BrainNetwork class into Weighted and Binary subclasses
ccd055e
@Islast
Merge branch 'paired-brains' of github.com:WhitakerLab/scona into pai…
42af7d1
…red-brains
@Islast
add split_groups function
5234b79
@Islast
add shuffleing to split_groups
fe91cfd
@KirstieJane
Add comments
309951a
@Islast
copy dataframe
360e7cf
@KirstieJane
Fix merge conflicts
e582376
Add comments, slightly restructure
@KirstieJane
First commit of tutorial to compare groups
4b1a44c
@KirstieJane
Add comments
3091d30
@Islast
implement patient grouping at correlation matrix level
8d72ba5
@Islast
unify parsers and install command line tools at setup
e54952b
@Islast
structure setup to install command line tools
960bc88
@Islast
unify parsers and install command line tools at setup
0cf0a26
@Islast
structure setup to install command line tools
1952f9e
@Islast
Merge branch 'commandline' of github.com:Islast/scona into commandline
7b4b8c5
@Islast
add split_groups function
d3f54eb
@Islast
add shuffleing to split_groups
640983d
@Islast
rebase onto master
8ddaaea
@KirstieJane@Islast
First commit of tutorial to compare groups
483c527
@Islast
implement patient grouping at correlation matrix level
e27bbf4
@Islast
better syntax for boolean evaluation
a731e9d
@Islast
Merge branch 'paired-brains' of github.com:Islast/scona into paired-b…
8385d93
…rains
@Islast
fix syntax error
92a392a
@Islast
Merge branch 'commandline' into paired-brains
a51eff3
@Islast
variable renaming
8b251ea
@Islast
replace scona.py wrapper
c2fb702
@Islast
writing out corrmat now optional
368c3df
@Islast
regression test command line tool
292f8b7
@Islast
add split_groups function
71ec9c9
@Islast
add shuffleing to split_groups
6ffcb6d
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2 participants

@Islast@KirstieJane

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Split brain networks by Islast · Pull Request #125 · WhitakerLab/scona · GitHub
Skip to content
Split brain networks - #125
Open
Islast wants to merge 47 commits into
WhitakerLab:masterfrom 
Islast:splitBrainNetworks
Open
Split brain networks#125
Islast wants to merge 47 commits into
WhitakerLab:masterfrom 
Islast:splitBrainNetworks
Conversation
@Islast
@IslastIslast
commented
Jul 4, 2019

Copy link


Copy Markdown

Collaborator
  •  I'm ready to merge
    
Not at all. This is just a preview of my proposed changes to seperate the BrainNetwork class into two distinct subclasses: BinaryBrainNetwork and WeightedBrainNetwork.
  • What's the context for this pull request?
    (this is a good place to reference any issues that this PR addresses)
    
Ruslan discovered that when you run the threshold method on an already binarised graph it returns garbage.
    
This made me think that there are potentially a lot of situations where treated a weighted network like a binary network or vice versa could be disastrous.
  • What's new?
    
My thinking is that the difference between a weighted and a binarised brain network should be very explicit since it's going to determine what sort of analyses we can do on it.
It should be possible to threshold a WeightedBrainNetwork into a BinaryBrainNetwork and it should be possible to initialise a WeightedBrainNetwork from a correlation matrix.
A BinaryBrainNetwork should support all of the network analysis methods. We could run these on a weighted graph no problem, but they would tell us nothing about our data. We will record the original weightings on existent BinaryBrainNetworks in case we want to restrict our focus to fewer edges later (the specific use case being plotting).
  • What should a reviewer feedback on?
    
Is this the right direction to go in to solve this problem.
  • Does anything need to be updated after merge?
    (e.g the wiki or the WhitakerLab website)
docs and tutorials would certainly need to be updated, but it's a little early for that.
Islastand others
added 30 commits
July 3, 2019 19:30
@Islast
Split BrainNetwork class into Weighted and Binary subclasses
ccd055e
@Islast
Merge branch 'paired-brains' of github.com:WhitakerLab/scona into pai…
42af7d1
…red-brains
@Islast
add split_groups function
5234b79
@Islast
add shuffleing to split_groups
fe91cfd
@KirstieJane
Add comments
309951a
@Islast
copy dataframe
360e7cf
@KirstieJane
Fix merge conflicts
e582376
Add comments, slightly restructure
@KirstieJane
First commit of tutorial to compare groups
4b1a44c
@KirstieJane
Add comments
3091d30
@Islast
implement patient grouping at correlation matrix level
8d72ba5
@Islast
unify parsers and install command line tools at setup
e54952b
@Islast
structure setup to install command line tools
960bc88
@Islast
unify parsers and install command line tools at setup
0cf0a26
@Islast
structure setup to install command line tools
1952f9e
@Islast
Merge branch 'commandline' of github.com:Islast/scona into commandline
7b4b8c5
@Islast
add split_groups function
d3f54eb
@Islast
add shuffleing to split_groups
640983d
@Islast
rebase onto master
8ddaaea
@KirstieJane@Islast
First commit of tutorial to compare groups
483c527
@Islast
implement patient grouping at correlation matrix level
e27bbf4
@Islast
better syntax for boolean evaluation
a731e9d
@Islast
Merge branch 'paired-brains' of github.com:Islast/scona into paired-b…
8385d93
…rains
@Islast
fix syntax error
92a392a
@Islast
Merge branch 'commandline' into paired-brains
a51eff3
@Islast
variable renaming
8b251ea
@Islast
replace scona.py wrapper
c2fb702
@Islast
writing out corrmat now optional
368c3df
@Islast
regression test command line tool
292f8b7
@Islast
add split_groups function
71ec9c9
@Islast
add shuffleing to split_groups
6ffcb6d
Sign up for freeto join this conversation on GitHub.
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2 participants

@Islast@KirstieJane

, 'i');
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Split brain networks by Islast · Pull Request #125 · WhitakerLab/scona · GitHub
Skip to content
Split brain networks - #125
Open
Islast wants to merge 47 commits into
WhitakerLab:masterfrom 
Islast:splitBrainNetworks
Open
Split brain networks#125
Islast wants to merge 47 commits into
WhitakerLab:masterfrom 
Islast:splitBrainNetworks
Conversation
@Islast
@IslastIslast
commented
Jul 4, 2019

Copy link


Copy Markdown

Collaborator
  •  I'm ready to merge
    
Not at all. This is just a preview of my proposed changes to seperate the BrainNetwork class into two distinct subclasses: BinaryBrainNetwork and WeightedBrainNetwork.
  • What's the context for this pull request?
    (this is a good place to reference any issues that this PR addresses)
    
Ruslan discovered that when you run the threshold method on an already binarised graph it returns garbage.
    
This made me think that there are potentially a lot of situations where treated a weighted network like a binary network or vice versa could be disastrous.
  • What's new?
    
My thinking is that the difference between a weighted and a binarised brain network should be very explicit since it's going to determine what sort of analyses we can do on it.
It should be possible to threshold a WeightedBrainNetwork into a BinaryBrainNetwork and it should be possible to initialise a WeightedBrainNetwork from a correlation matrix.
A BinaryBrainNetwork should support all of the network analysis methods. We could run these on a weighted graph no problem, but they would tell us nothing about our data. We will record the original weightings on existent BinaryBrainNetworks in case we want to restrict our focus to fewer edges later (the specific use case being plotting).
  • What should a reviewer feedback on?
    
Is this the right direction to go in to solve this problem.
  • Does anything need to be updated after merge?
    (e.g the wiki or the WhitakerLab website)
docs and tutorials would certainly need to be updated, but it's a little early for that.
Islastand others
added 30 commits
July 3, 2019 19:30
@Islast
Split BrainNetwork class into Weighted and Binary subclasses
ccd055e
@Islast
Merge branch 'paired-brains' of github.com:WhitakerLab/scona into pai…
42af7d1
…red-brains
@Islast
add split_groups function
5234b79
@Islast
add shuffleing to split_groups
fe91cfd
@KirstieJane
Add comments
309951a
@Islast
copy dataframe
360e7cf
@KirstieJane
Fix merge conflicts
e582376
Add comments, slightly restructure
@KirstieJane
First commit of tutorial to compare groups
4b1a44c
@KirstieJane
Add comments
3091d30
@Islast
implement patient grouping at correlation matrix level
8d72ba5
@Islast
unify parsers and install command line tools at setup
e54952b
@Islast
structure setup to install command line tools
960bc88
@Islast
unify parsers and install command line tools at setup
0cf0a26
@Islast
structure setup to install command line tools
1952f9e
@Islast
Merge branch 'commandline' of github.com:Islast/scona into commandline
7b4b8c5
@Islast
add split_groups function
d3f54eb
@Islast
add shuffleing to split_groups
640983d
@Islast
rebase onto master
8ddaaea
@KirstieJane@Islast
First commit of tutorial to compare groups
483c527
@Islast
implement patient grouping at correlation matrix level
e27bbf4
@Islast
better syntax for boolean evaluation
a731e9d
@Islast
Merge branch 'paired-brains' of github.com:Islast/scona into paired-b…
8385d93
…rains
@Islast
fix syntax error
92a392a
@Islast
Merge branch 'commandline' into paired-brains
a51eff3
@Islast
variable renaming
8b251ea
@Islast
replace scona.py wrapper
c2fb702
@Islast
writing out corrmat now optional
368c3df
@Islast
regression test command line tool
292f8b7
@Islast
add split_groups function
71ec9c9
@Islast
add shuffleing to split_groups
6ffcb6d
Sign up for freeto join this conversation on GitHub.
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Development

Successfully merging this pull request may close these issues.

2 participants

@Islast@KirstieJane

, 'i');
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Split brain networks by Islast · Pull Request #125 · WhitakerLab/scona · GitHub
Skip to content
Split brain networks - #125
Open
Islast wants to merge 47 commits into
WhitakerLab:masterfrom 
Islast:splitBrainNetworks
Open
Split brain networks#125
Islast wants to merge 47 commits into
WhitakerLab:masterfrom 
Islast:splitBrainNetworks
Conversation
@Islast
@IslastIslast
commented
Jul 4, 2019

Copy link


Copy Markdown

Collaborator
  •  I'm ready to merge
    
Not at all. This is just a preview of my proposed changes to seperate the BrainNetwork class into two distinct subclasses: BinaryBrainNetwork and WeightedBrainNetwork.
  • What's the context for this pull request?
    (this is a good place to reference any issues that this PR addresses)
    
Ruslan discovered that when you run the threshold method on an already binarised graph it returns garbage.
    
This made me think that there are potentially a lot of situations where treated a weighted network like a binary network or vice versa could be disastrous.
  • What's new?
    
My thinking is that the difference between a weighted and a binarised brain network should be very explicit since it's going to determine what sort of analyses we can do on it.
It should be possible to threshold a WeightedBrainNetwork into a BinaryBrainNetwork and it should be possible to initialise a WeightedBrainNetwork from a correlation matrix.
A BinaryBrainNetwork should support all of the network analysis methods. We could run these on a weighted graph no problem, but they would tell us nothing about our data. We will record the original weightings on existent BinaryBrainNetworks in case we want to restrict our focus to fewer edges later (the specific use case being plotting).
  • What should a reviewer feedback on?
    
Is this the right direction to go in to solve this problem.
  • Does anything need to be updated after merge?
    (e.g the wiki or the WhitakerLab website)
docs and tutorials would certainly need to be updated, but it's a little early for that.
Islastand others
added 30 commits
July 3, 2019 19:30
@Islast
Split BrainNetwork class into Weighted and Binary subclasses
ccd055e
@Islast
Merge branch 'paired-brains' of github.com:WhitakerLab/scona into pai…
42af7d1
…red-brains
@Islast
add split_groups function
5234b79
@Islast
add shuffleing to split_groups
fe91cfd
@KirstieJane
Add comments
309951a
@Islast
copy dataframe
360e7cf
@KirstieJane
Fix merge conflicts
e582376
Add comments, slightly restructure
@KirstieJane
First commit of tutorial to compare groups
4b1a44c
@KirstieJane
Add comments
3091d30
@Islast
implement patient grouping at correlation matrix level
8d72ba5
@Islast
unify parsers and install command line tools at setup
e54952b
@Islast
structure setup to install command line tools
960bc88
@Islast
unify parsers and install command line tools at setup
0cf0a26
@Islast
structure setup to install command line tools
1952f9e
@Islast
Merge branch 'commandline' of github.com:Islast/scona into commandline
7b4b8c5
@Islast
add split_groups function
d3f54eb
@Islast
add shuffleing to split_groups
640983d
@Islast
rebase onto master
8ddaaea
@KirstieJane@Islast
First commit of tutorial to compare groups
483c527
@Islast
implement patient grouping at correlation matrix level
e27bbf4
@Islast
better syntax for boolean evaluation
a731e9d
@Islast
Merge branch 'paired-brains' of github.com:Islast/scona into paired-b…
8385d93
…rains
@Islast
fix syntax error
92a392a
@Islast
Merge branch 'commandline' into paired-brains
a51eff3
@Islast
variable renaming
8b251ea
@Islast
replace scona.py wrapper
c2fb702
@Islast
writing out corrmat now optional
368c3df
@Islast
regression test command line tool
292f8b7
@Islast
add split_groups function
71ec9c9
@Islast
add shuffleing to split_groups
6ffcb6d
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@Islast@KirstieJane

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Split brain networks by Islast · Pull Request #125 · WhitakerLab/scona · GitHub
Skip to content
Split brain networks - #125
Open
Islast wants to merge 47 commits into
WhitakerLab:masterfrom 
Islast:splitBrainNetworks
Open
Split brain networks#125
Islast wants to merge 47 commits into
WhitakerLab:masterfrom 
Islast:splitBrainNetworks
Conversation
@Islast
@IslastIslast
commented
Jul 4, 2019

Copy link


Copy Markdown

Collaborator
  •  I'm ready to merge
    
Not at all. This is just a preview of my proposed changes to seperate the BrainNetwork class into two distinct subclasses: BinaryBrainNetwork and WeightedBrainNetwork.
  • What's the context for this pull request?
    (this is a good place to reference any issues that this PR addresses)
    
Ruslan discovered that when you run the threshold method on an already binarised graph it returns garbage.
    
This made me think that there are potentially a lot of situations where treated a weighted network like a binary network or vice versa could be disastrous.
  • What's new?
    
My thinking is that the difference between a weighted and a binarised brain network should be very explicit since it's going to determine what sort of analyses we can do on it.
It should be possible to threshold a WeightedBrainNetwork into a BinaryBrainNetwork and it should be possible to initialise a WeightedBrainNetwork from a correlation matrix.
A BinaryBrainNetwork should support all of the network analysis methods. We could run these on a weighted graph no problem, but they would tell us nothing about our data. We will record the original weightings on existent BinaryBrainNetworks in case we want to restrict our focus to fewer edges later (the specific use case being plotting).
  • What should a reviewer feedback on?
    
Is this the right direction to go in to solve this problem.
  • Does anything need to be updated after merge?
    (e.g the wiki or the WhitakerLab website)
docs and tutorials would certainly need to be updated, but it's a little early for that.
Islastand others
added 30 commits
July 3, 2019 19:30
@Islast
Split BrainNetwork class into Weighted and Binary subclasses
ccd055e
@Islast
Merge branch 'paired-brains' of github.com:WhitakerLab/scona into pai…
42af7d1
…red-brains
@Islast
add split_groups function
5234b79
@Islast
add shuffleing to split_groups
fe91cfd
@KirstieJane
Add comments
309951a
@Islast
copy dataframe
360e7cf
@KirstieJane
Fix merge conflicts
e582376
Add comments, slightly restructure
@KirstieJane
First commit of tutorial to compare groups
4b1a44c
@KirstieJane
Add comments
3091d30
@Islast
implement patient grouping at correlation matrix level
8d72ba5
@Islast
unify parsers and install command line tools at setup
e54952b
@Islast
structure setup to install command line tools
960bc88
@Islast
unify parsers and install command line tools at setup
0cf0a26
@Islast
structure setup to install command line tools
1952f9e
@Islast
Merge branch 'commandline' of github.com:Islast/scona into commandline
7b4b8c5
@Islast
add split_groups function
d3f54eb
@Islast
add shuffleing to split_groups
640983d
@Islast
rebase onto master
8ddaaea
@KirstieJane@Islast
First commit of tutorial to compare groups
483c527
@Islast
implement patient grouping at correlation matrix level
e27bbf4
@Islast
better syntax for boolean evaluation
a731e9d
@Islast
Merge branch 'paired-brains' of github.com:Islast/scona into paired-b…
8385d93
…rains
@Islast
fix syntax error
92a392a
@Islast
Merge branch 'commandline' into paired-brains
a51eff3
@Islast
variable renaming
8b251ea
@Islast
replace scona.py wrapper
c2fb702
@Islast
writing out corrmat now optional
368c3df
@Islast
regression test command line tool
292f8b7
@Islast
add split_groups function
71ec9c9
@Islast
add shuffleing to split_groups
6ffcb6d
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2 participants

@Islast@KirstieJane

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Split brain networks by Islast · Pull Request #125 · WhitakerLab/scona · GitHub
Skip to content
Split brain networks - #125
Open
Islast wants to merge 47 commits into
WhitakerLab:masterfrom 
Islast:splitBrainNetworks
Open
Split brain networks#125
Islast wants to merge 47 commits into
WhitakerLab:masterfrom 
Islast:splitBrainNetworks
Conversation
@Islast
@IslastIslast
commented
Jul 4, 2019

Copy link


Copy Markdown

Collaborator
  •  I'm ready to merge
    
Not at all. This is just a preview of my proposed changes to seperate the BrainNetwork class into two distinct subclasses: BinaryBrainNetwork and WeightedBrainNetwork.
  • What's the context for this pull request?
    (this is a good place to reference any issues that this PR addresses)
    
Ruslan discovered that when you run the threshold method on an already binarised graph it returns garbage.
    
This made me think that there are potentially a lot of situations where treated a weighted network like a binary network or vice versa could be disastrous.
  • What's new?
    
My thinking is that the difference between a weighted and a binarised brain network should be very explicit since it's going to determine what sort of analyses we can do on it.
It should be possible to threshold a WeightedBrainNetwork into a BinaryBrainNetwork and it should be possible to initialise a WeightedBrainNetwork from a correlation matrix.
A BinaryBrainNetwork should support all of the network analysis methods. We could run these on a weighted graph no problem, but they would tell us nothing about our data. We will record the original weightings on existent BinaryBrainNetworks in case we want to restrict our focus to fewer edges later (the specific use case being plotting).
  • What should a reviewer feedback on?
    
Is this the right direction to go in to solve this problem.
  • Does anything need to be updated after merge?
    (e.g the wiki or the WhitakerLab website)
docs and tutorials would certainly need to be updated, but it's a little early for that.
Islastand others
added 30 commits
July 3, 2019 19:30
@Islast
Split BrainNetwork class into Weighted and Binary subclasses
ccd055e
@Islast
Merge branch 'paired-brains' of github.com:WhitakerLab/scona into pai…
42af7d1
…red-brains
@Islast
add split_groups function
5234b79
@Islast
add shuffleing to split_groups
fe91cfd
@KirstieJane
Add comments
309951a
@Islast
copy dataframe
360e7cf
@KirstieJane
Fix merge conflicts
e582376
Add comments, slightly restructure
@KirstieJane
First commit of tutorial to compare groups
4b1a44c
@KirstieJane
Add comments
3091d30
@Islast
implement patient grouping at correlation matrix level
8d72ba5
@Islast
unify parsers and install command line tools at setup
e54952b
@Islast
structure setup to install command line tools
960bc88
@Islast
unify parsers and install command line tools at setup
0cf0a26
@Islast
structure setup to install command line tools
1952f9e
@Islast
Merge branch 'commandline' of github.com:Islast/scona into commandline
7b4b8c5
@Islast
add split_groups function
d3f54eb
@Islast
add shuffleing to split_groups
640983d
@Islast
rebase onto master
8ddaaea
@KirstieJane@Islast
First commit of tutorial to compare groups
483c527
@Islast
implement patient grouping at correlation matrix level
e27bbf4
@Islast
better syntax for boolean evaluation
a731e9d
@Islast
Merge branch 'paired-brains' of github.com:Islast/scona into paired-b…
8385d93
…rains
@Islast
fix syntax error
92a392a
@Islast
Merge branch 'commandline' into paired-brains
a51eff3
@Islast
variable renaming
8b251ea
@Islast
replace scona.py wrapper
c2fb702
@Islast
writing out corrmat now optional
368c3df
@Islast
regression test command line tool
292f8b7
@Islast
add split_groups function
71ec9c9
@Islast
add shuffleing to split_groups
6ffcb6d
Sign up for freeto join this conversation on GitHub.
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Development

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2 participants

@Islast@KirstieJane

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Split brain networks by Islast · Pull Request #125 · WhitakerLab/scona · GitHub
Skip to content
Split brain networks - #125
Open
Islast wants to merge 47 commits into
WhitakerLab:masterfrom 
Islast:splitBrainNetworks
Open
Split brain networks#125
Islast wants to merge 47 commits into
WhitakerLab:masterfrom 
Islast:splitBrainNetworks
Conversation
@Islast
@IslastIslast
commented
Jul 4, 2019

Copy link


Copy Markdown

Collaborator
  •  I'm ready to merge
    
Not at all. This is just a preview of my proposed changes to seperate the BrainNetwork class into two distinct subclasses: BinaryBrainNetwork and WeightedBrainNetwork.
  • What's the context for this pull request?
    (this is a good place to reference any issues that this PR addresses)
    
Ruslan discovered that when you run the threshold method on an already binarised graph it returns garbage.
    
This made me think that there are potentially a lot of situations where treated a weighted network like a binary network or vice versa could be disastrous.
  • What's new?
    
My thinking is that the difference between a weighted and a binarised brain network should be very explicit since it's going to determine what sort of analyses we can do on it.
It should be possible to threshold a WeightedBrainNetwork into a BinaryBrainNetwork and it should be possible to initialise a WeightedBrainNetwork from a correlation matrix.
A BinaryBrainNetwork should support all of the network analysis methods. We could run these on a weighted graph no problem, but they would tell us nothing about our data. We will record the original weightings on existent BinaryBrainNetworks in case we want to restrict our focus to fewer edges later (the specific use case being plotting).
  • What should a reviewer feedback on?
    
Is this the right direction to go in to solve this problem.
  • Does anything need to be updated after merge?
    (e.g the wiki or the WhitakerLab website)
docs and tutorials would certainly need to be updated, but it's a little early for that.
Islastand others
added 30 commits
July 3, 2019 19:30
@Islast
Split BrainNetwork class into Weighted and Binary subclasses
ccd055e
@Islast
Merge branch 'paired-brains' of github.com:WhitakerLab/scona into pai…
42af7d1
…red-brains
@Islast
add split_groups function
5234b79
@Islast
add shuffleing to split_groups
fe91cfd
@KirstieJane
Add comments
309951a
@Islast
copy dataframe
360e7cf
@KirstieJane
Fix merge conflicts
e582376
Add comments, slightly restructure
@KirstieJane
First commit of tutorial to compare groups
4b1a44c
@KirstieJane
Add comments
3091d30
@Islast
implement patient grouping at correlation matrix level
8d72ba5
@Islast
unify parsers and install command line tools at setup
e54952b
@Islast
structure setup to install command line tools
960bc88
@Islast
unify parsers and install command line tools at setup
0cf0a26
@Islast
structure setup to install command line tools
1952f9e
@Islast
Merge branch 'commandline' of github.com:Islast/scona into commandline
7b4b8c5
@Islast
add split_groups function
d3f54eb
@Islast
add shuffleing to split_groups
640983d
@Islast
rebase onto master
8ddaaea
@KirstieJane@Islast
First commit of tutorial to compare groups
483c527
@Islast
implement patient grouping at correlation matrix level
e27bbf4
@Islast
better syntax for boolean evaluation
a731e9d
@Islast
Merge branch 'paired-brains' of github.com:Islast/scona into paired-b…
8385d93
…rains
@Islast
fix syntax error
92a392a
@Islast
Merge branch 'commandline' into paired-brains
a51eff3
@Islast
variable renaming
8b251ea
@Islast
replace scona.py wrapper
c2fb702
@Islast
writing out corrmat now optional
368c3df
@Islast
regression test command line tool
292f8b7
@Islast
add split_groups function
71ec9c9
@Islast
add shuffleing to split_groups
6ffcb6d
Sign up for freeto join this conversation on GitHub.
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2 participants

@Islast@KirstieJane