Addition of constellation homologies workflow with tutorials#690
Merged
nfahlgren merged 56 commits intodanforthcenter:4.xfrom Sep 20, 2021
Merged
Addition of constellation homologies workflow with tutorials#690nfahlgren merged 56 commits intodanforthcenter:4.xfrom
nfahlgren merged 56 commits intodanforthcenter:4.xfrom
Conversation
Created plm_homologies directory containing de novo homology pipeline and migrated acute into this directory.
Cleaned up names of functions being called by init so that import of plm_homologies is successful.
The base functions required for homology grouping (space [optional], starscape, and constella as well as a QC screening script (constellaQC) have been added via the homology module in PCV. Markdown files have also been added which present the implementation of acute (tutorials 1 & 2) as well as the usage of homology on segmented plant data (tutorials 3 & 4).
Adjusting format size of graphs for ease of better display purposes.
Moving existing .md files from ~/docs/ to ~/docs/tutorials/ for the plm analysis and homology workflow.
Member
|
@jgerardhodge is the new pull request just for merging with 4.x? If so, we can update this PR to compare to 4.x instead |
nfahlgren
added
new feature
Python convention is lowercase variable names
float(len(acute_pos)) / float(len(obj)) was not assigned to a variable and acute_pos was only used in that calculation
Codecov Report
@@ Coverage Diff @@
## 4.x #690 +/- ##
==========================================
Coverage 100.00% 100.00%
==========================================
Files 145 150 +5
Lines 6400 6631 +231
==========================================
+ Hits 6400 6631 +231
Flags with carried forward coverage won't be shown. Click here to find out more.
|
In our testing we could not trigger either condition and originally had this commented out in `pcv.acute`
Reduces code and testing complexity
I broke it when changing to is/is not because of how the NumPy comparisons need to be done
nfahlgren
added
ready to review
and removed
work in progress
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Describe your changes
Adds new functions under the homology module of PlantCV which consists of:
*space - generates additional metavariables for acute pseudo-landmarks
*starscape - function for dimensionality reduction of segmented plant data to generate constellations of points in a time series step
*constella - function for de novo homology grouping of nearest neighbors in these constellations through agglomerative clustering
*constellaQC - scores homology groupings against a known standard to estimate valid call rates in addition to clumping and splitting errors.
While space and constellaQC are considered optional functions due to their limited scope for datatypes or utility as QC measures respectively starscape and constella comprise the bulk of the constellation approach to de novo homology assessment.
In addition 4 tutorial md files have been included which form a series of "acute_plm_tutorial". The first two tutorials demonstrate the usage of acute for pseudo-landmarking as well as an implementation for running this script on batch datasets. The second two tutorials (i.e. 3 & 4) consist of a demonstration of the constellation grouping methodology on this simplified dataset as well as best practices for it's usage.
Type of update
Is this a:
Associated issues
Reference associated issue numbers. Does this pull request close any issues?
Additional context
Add any other context about the problem here.