Implementation of anatomical network visualisations by wingedRuslan · Pull Request #140 · WhitakerLab/scona

wingedRuslan · 2019-07-17T15:47:22Z

I'm ready to merge

What's the context for this pull request?
(this is a good place to reference any issues that this PR addresses)

Created plotting anatomical network functionality
Issues: #126, #122

What's new?
plot_anatomical_network function (+ some visualisation_helpers functions) and the tutorial to illustrate how to use new tools
What should a reviewer feedback on?
Is documentation clear?
Are the produced (and saved into a file) plots publication-ready and look nice?
Does anything need to be updated after merge?
(e.g the wiki or the WhitakerLab website)
Info on the website will be automatically updated

…DataFrame object and PathToFile

…ing a TypeError if unsupported type provided

…club function

…e - scona.visualisations

…rder to improve the process of saving a figure to file.

…e as a parameter

… function

…ction

…raphBundle as a parameter

…nction

…network_measures()

… change calc_nodal_measures in calculate_nodal_measures function

…ingedRuslan-master

I've made a whole bunch of changes to the jupyter notebook...but they're all just "yes, and"-ing the work that wingedRuslan did! So it looks like a big diff, and it kinda is, but very much only on a surface level <3

This is mostly a style and readability update... I found the print outs of the warnings a little hard to parse in the jupyter notebook and then I've changed the comments to better fit my understanding of what was happening.

Makes sense to set those early, especially if there's going to be a warning that folks want to understand.

Kirstie review of visualisation tutorial

…according to the given orientation

…er value to make results reproducible

…pers

…eptable one for seaborn.barplot

…orks

Islast · 2019-07-31T18:12:05Z

link to compare nx plotting branch to Ruslan master branch (eg PR 121)
All changes here seem absolutely fine

… well-connected nodes

wingedRuslan · 2019-07-17T15:47:22Z

I'm ready to merge

What's the context for this pull request?
(this is a good place to reference any issues that this PR addresses)

Created plotting anatomical network functionality
Issues: #126, #122

What's new?
plot_anatomical_network function (+ some visualisation_helpers functions) and the tutorial to illustrate how to use new tools
What should a reviewer feedback on?
Is documentation clear?
Are the produced (and saved into a file) plots publication-ready and look nice?
Does anything need to be updated after merge?
(e.g the wiki or the WhitakerLab website)
Info on the website will be automatically updated

…DataFrame object and PathToFile

…ing a TypeError if unsupported type provided

…club function

…e - scona.visualisations

…rder to improve the process of saving a figure to file.

…e as a parameter

… function

…ction

…raphBundle as a parameter

…nction

…network_measures()

… change calc_nodal_measures in calculate_nodal_measures function

…ingedRuslan-master

I've made a whole bunch of changes to the jupyter notebook...but they're all just "yes, and"-ing the work that wingedRuslan did! So it looks like a big diff, and it kinda is, but very much only on a surface level <3

This is mostly a style and readability update... I found the print outs of the warnings a little hard to parse in the jupyter notebook and then I've changed the comments to better fit my understanding of what was happening.

Makes sense to set those early, especially if there's going to be a warning that folks want to understand.

Kirstie review of visualisation tutorial

…according to the given orientation

…er value to make results reproducible

…pers

…eptable one for seaborn.barplot

…orks

Islast · 2019-07-31T18:12:05Z

link to compare nx plotting branch to Ruslan master branch (eg PR 121)
All changes here seem absolutely fine

… well-connected nodes

wingedRuslan · 2019-07-17T15:47:22Z

I'm ready to merge

What's the context for this pull request?
(this is a good place to reference any issues that this PR addresses)

Created plotting anatomical network functionality
Issues: #126, #122

What's new?
plot_anatomical_network function (+ some visualisation_helpers functions) and the tutorial to illustrate how to use new tools
What should a reviewer feedback on?
Is documentation clear?
Are the produced (and saved into a file) plots publication-ready and look nice?
Does anything need to be updated after merge?
(e.g the wiki or the WhitakerLab website)
Info on the website will be automatically updated

…DataFrame object and PathToFile

…ing a TypeError if unsupported type provided

…club function

…e - scona.visualisations

…rder to improve the process of saving a figure to file.

…e as a parameter

… function

…ction

…raphBundle as a parameter

…nction

…network_measures()

… change calc_nodal_measures in calculate_nodal_measures function

…ingedRuslan-master

I've made a whole bunch of changes to the jupyter notebook...but they're all just "yes, and"-ing the work that wingedRuslan did! So it looks like a big diff, and it kinda is, but very much only on a surface level <3

This is mostly a style and readability update... I found the print outs of the warnings a little hard to parse in the jupyter notebook and then I've changed the comments to better fit my understanding of what was happening.

Makes sense to set those early, especially if there's going to be a warning that folks want to understand.

Kirstie review of visualisation tutorial

…according to the given orientation

…er value to make results reproducible

…pers

…eptable one for seaborn.barplot

…orks

Islast · 2019-07-31T18:12:05Z

link to compare nx plotting branch to Ruslan master branch (eg PR 121)
All changes here seem absolutely fine

… well-connected nodes

wingedRuslan · 2019-07-17T15:47:22Z

I'm ready to merge

What's the context for this pull request?
(this is a good place to reference any issues that this PR addresses)

Created plotting anatomical network functionality
Issues: #126, #122

What's new?
plot_anatomical_network function (+ some visualisation_helpers functions) and the tutorial to illustrate how to use new tools
What should a reviewer feedback on?
Is documentation clear?
Are the produced (and saved into a file) plots publication-ready and look nice?
Does anything need to be updated after merge?
(e.g the wiki or the WhitakerLab website)
Info on the website will be automatically updated

…DataFrame object and PathToFile

…ing a TypeError if unsupported type provided

…club function

…e - scona.visualisations

…rder to improve the process of saving a figure to file.

…e as a parameter

… function

…ction

…raphBundle as a parameter

…nction

…network_measures()

… change calc_nodal_measures in calculate_nodal_measures function

…ingedRuslan-master

I've made a whole bunch of changes to the jupyter notebook...but they're all just "yes, and"-ing the work that wingedRuslan did! So it looks like a big diff, and it kinda is, but very much only on a surface level <3

This is mostly a style and readability update... I found the print outs of the warnings a little hard to parse in the jupyter notebook and then I've changed the comments to better fit my understanding of what was happening.

Makes sense to set those early, especially if there's going to be a warning that folks want to understand.

Kirstie review of visualisation tutorial

…according to the given orientation

…er value to make results reproducible

…pers

…eptable one for seaborn.barplot

…orks

Islast · 2019-07-31T18:12:05Z

link to compare nx plotting branch to Ruslan master branch (eg PR 121)
All changes here seem absolutely fine

… well-connected nodes

wingedRuslan · 2019-07-17T15:47:22Z

I'm ready to merge

What's the context for this pull request?
(this is a good place to reference any issues that this PR addresses)

Created plotting anatomical network functionality
Issues: #126, #122

What's new?
plot_anatomical_network function (+ some visualisation_helpers functions) and the tutorial to illustrate how to use new tools
What should a reviewer feedback on?
Is documentation clear?
Are the produced (and saved into a file) plots publication-ready and look nice?
Does anything need to be updated after merge?
(e.g the wiki or the WhitakerLab website)
Info on the website will be automatically updated

…DataFrame object and PathToFile

…ing a TypeError if unsupported type provided

…club function

…e - scona.visualisations

…rder to improve the process of saving a figure to file.

…e as a parameter

… function

…ction

…raphBundle as a parameter

…nction

…network_measures()

… change calc_nodal_measures in calculate_nodal_measures function

…ingedRuslan-master

I've made a whole bunch of changes to the jupyter notebook...but they're all just "yes, and"-ing the work that wingedRuslan did! So it looks like a big diff, and it kinda is, but very much only on a surface level <3

This is mostly a style and readability update... I found the print outs of the warnings a little hard to parse in the jupyter notebook and then I've changed the comments to better fit my understanding of what was happening.

Makes sense to set those early, especially if there's going to be a warning that folks want to understand.

Kirstie review of visualisation tutorial

…according to the given orientation

…er value to make results reproducible

…pers

…eptable one for seaborn.barplot

…orks

Islast · 2019-07-31T18:12:05Z

link to compare nx plotting branch to Ruslan master branch (eg PR 121)
All changes here seem absolutely fine

… well-connected nodes

wingedRuslan · 2019-07-17T15:47:22Z

I'm ready to merge

What's the context for this pull request?
(this is a good place to reference any issues that this PR addresses)

Created plotting anatomical network functionality
Issues: #126, #122

What's new?
plot_anatomical_network function (+ some visualisation_helpers functions) and the tutorial to illustrate how to use new tools
What should a reviewer feedback on?
Is documentation clear?
Are the produced (and saved into a file) plots publication-ready and look nice?
Does anything need to be updated after merge?
(e.g the wiki or the WhitakerLab website)
Info on the website will be automatically updated

…DataFrame object and PathToFile

…ing a TypeError if unsupported type provided

…club function

…e - scona.visualisations

…rder to improve the process of saving a figure to file.

…e as a parameter

… function

…ction

…raphBundle as a parameter

…nction

…network_measures()

… change calc_nodal_measures in calculate_nodal_measures function

…ingedRuslan-master

I've made a whole bunch of changes to the jupyter notebook...but they're all just "yes, and"-ing the work that wingedRuslan did! So it looks like a big diff, and it kinda is, but very much only on a surface level <3

This is mostly a style and readability update... I found the print outs of the warnings a little hard to parse in the jupyter notebook and then I've changed the comments to better fit my understanding of what was happening.

Makes sense to set those early, especially if there's going to be a warning that folks want to understand.

Kirstie review of visualisation tutorial

…according to the given orientation

…er value to make results reproducible

…pers

…eptable one for seaborn.barplot

…orks

Islast · 2019-07-31T18:12:05Z

link to compare nx plotting branch to Ruslan master branch (eg PR 121)
All changes here seem absolutely fine

… well-connected nodes

wingedRuslan · 2019-07-17T15:47:22Z

I'm ready to merge

What's the context for this pull request?
(this is a good place to reference any issues that this PR addresses)

Created plotting anatomical network functionality
Issues: #126, #122

What's new?
plot_anatomical_network function (+ some visualisation_helpers functions) and the tutorial to illustrate how to use new tools
What should a reviewer feedback on?
Is documentation clear?
Are the produced (and saved into a file) plots publication-ready and look nice?
Does anything need to be updated after merge?
(e.g the wiki or the WhitakerLab website)
Info on the website will be automatically updated

…DataFrame object and PathToFile

…ing a TypeError if unsupported type provided

…club function

…e - scona.visualisations

…rder to improve the process of saving a figure to file.

…e as a parameter

… function

…ction

…raphBundle as a parameter

…nction

…network_measures()

… change calc_nodal_measures in calculate_nodal_measures function

…ingedRuslan-master

I've made a whole bunch of changes to the jupyter notebook...but they're all just "yes, and"-ing the work that wingedRuslan did! So it looks like a big diff, and it kinda is, but very much only on a surface level <3

This is mostly a style and readability update... I found the print outs of the warnings a little hard to parse in the jupyter notebook and then I've changed the comments to better fit my understanding of what was happening.

Makes sense to set those early, especially if there's going to be a warning that folks want to understand.

Kirstie review of visualisation tutorial

…according to the given orientation

…er value to make results reproducible

…pers

…eptable one for seaborn.barplot

…orks

Islast · 2019-07-31T18:12:05Z

link to compare nx plotting branch to Ruslan master branch (eg PR 121)
All changes here seem absolutely fine

… well-connected nodes

wingedRuslan · 2019-07-17T15:47:22Z

I'm ready to merge

What's the context for this pull request?
(this is a good place to reference any issues that this PR addresses)

Created plotting anatomical network functionality
Issues: #126, #122

What's new?
plot_anatomical_network function (+ some visualisation_helpers functions) and the tutorial to illustrate how to use new tools
What should a reviewer feedback on?
Is documentation clear?
Are the produced (and saved into a file) plots publication-ready and look nice?
Does anything need to be updated after merge?
(e.g the wiki or the WhitakerLab website)
Info on the website will be automatically updated

…DataFrame object and PathToFile

…ing a TypeError if unsupported type provided

…club function

…e - scona.visualisations

…rder to improve the process of saving a figure to file.

…e as a parameter

… function

…ction

…raphBundle as a parameter

…nction

…network_measures()

… change calc_nodal_measures in calculate_nodal_measures function

…ingedRuslan-master

I've made a whole bunch of changes to the jupyter notebook...but they're all just "yes, and"-ing the work that wingedRuslan did! So it looks like a big diff, and it kinda is, but very much only on a surface level <3

This is mostly a style and readability update... I found the print outs of the warnings a little hard to parse in the jupyter notebook and then I've changed the comments to better fit my understanding of what was happening.

Makes sense to set those early, especially if there's going to be a warning that folks want to understand.

Kirstie review of visualisation tutorial

…according to the given orientation

…er value to make results reproducible

…pers

…eptable one for seaborn.barplot

…orks

Islast · 2019-07-31T18:12:05Z

link to compare nx plotting branch to Ruslan master branch (eg PR 121)
All changes here seem absolutely fine

… well-connected nodes

wingedRuslanand others added 30 commits April 2, 2019 23:12

Try to link to autodoc content in the introduction.rst
0cb64ab

Add documentation to the introduction page
86ff8d6

Add documentation to the introduction page, ready for PR
1500c32

Merge branch 'master' ofhttps://github.com/wingedRuslan/scona
5412842

Update view_corr_mat in visualisation commands to accept corr_mat as …
9d083dc
…DataFrame object and PathToFile

Add support of numpy.array as an input for view_corr_mat and add rais…
d93b9fe
…ing a TypeError if unsupported type provided

Check that corr_mat is n x n matrix, otherwise raise Error
d9ed917

Explain corr_mat argument to view_corr_mat() more precisely
f9fe78c

Merge remote-tracking branch 'upstream/master'
2d76afb

Created a new file for visualisation tools and implemented plot_rich_…
0d5155d
…club function

Main implementation of plot_network_measures function
b050a7e

Implemention of plot_network_measures function
28ff8e5

Implementation of plot_degree_dist function
4438537

Update source file for sphinx auto documentation to include new modul…
287260f
…e - scona.visualisations

Add tutorial to show how to use created visualisation tools
eb3e549

Address PR#121 comments. Create in scona/helpers.py <save_fig()> in o…
cdd9acc
…rder to improve the process of saving a figure to file.

Address PR#121 comments. Modify plot_rich_club() to accept GraphBundl…
5b8107d
…e as a parameter

Update the visualisation tutorial based on the updated plot_rich_club…
aa34567
… function

Fix bugs in saving figures function and in plotting degree distribution
8426955

Update the visualisation tutorial to demonstrate plot_degree_dist fun…
adb4347
…ction

Address PR#121 comments. Redesign plot_network_measures() to accept G…
a97c24e
…raphBundle as a parameter

Update plot_rich_club to accept real_network as a parameter to the fu…
1f2c1aa
…nction

Update the visualisation_tutorial to show the usage of modified plot_…
20d6f74
…network_measures()

Update the documentation about GraphBundle, report_global_measures &&…
da7a994
… change calc_nodal_measures in calculate_nodal_measures function

Merge branch 'master' ofhttps://github.com/wingedRuslan/sconainto w…
b6fdd17
…ingedRuslan-master

Refactor (opinionated Kirstie)
064bad0
I've made a whole bunch of changes to the jupyter notebook...but they're all just "yes, and"-ing the work that wingedRuslan did! So it looks like a big diff, and it kinda is, but very much only on a surface level <3

Ignore figures directory when tutorials are run
70080fc

Adjust comments
ece228f
This is mostly a style and readability update... I found the print outs of the warnings a little hard to parse in the jupyter notebook and then I've changed the comments to better fit my understanding of what was happening.

Move color settings earlier in function
da1a611
Makes sense to set those early, especially if there's going to be a warning that folks want to understand.

Merge pull request#2from WhitakerLab/kw-visualisation
73214a5
Kirstie review of visualisation tutorial

wingedRuslan added 12 commits July 6, 2019 23:06

Implemented setup_color_list() to get list of colors for each data value
4e2a04b

Implemented add_colorbar() to have the ability to add colorbar to plot
1fd0019

Merge the changes Kirstie made into my local master branch
e4b9782

Add anatomical_layout() as a helper function to get node coordinates …
da7e1d9
…according to the given orientation

WhitakerLab#130- In plot_degree_dist() set seed to the default integ…
116dc6d
…er value to make results reproducible

Renaming helpers.py to explicitly state that it is visualisations_hel…
64e3cc1
…pers

Create a function df_sns_barplot for restructuring DataFrame into acc…
7a9bcd4
…eptable one for seaborn.barplot

Create plotting anatomical network function
ae5e27f

Fix small bugs in plot_anatomical_network
37c27f8

Create a tutorial to show functionalities of plotting anatomical netw…
a48a226
…orks

Adjust the sizes of produced plots, add border for node when displayed
3bc48d3

Update tutorial to show changes made in plot_anatomical_network
26a26ad

Update network visualisations tutorial to fix a bug while calculating…
2b57b5c
… well-connected nodes

wingedRuslan requested a review from KirstieJane August 5, 2019 11:08

wingedRuslan mentioned this pull request Aug 12, 2019
Removing old viz modules #148
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