visualization.py #5
Open
Conversation
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
…into develop r: failed to push some refs to 'https://github.com/IEEE-Ege/SingleCellWebApp.git' hint: Updates were rejected because the remote contains work that you do not hint: have locally. This is usually caused by another repository pushing to hint: the same ref. If you want to integrate the remote changes, use hint: 'git pull' before pushing again. hint: See the 'Note about fast-forwards' in 'git push --help' for details. solving conflicts
…election - Added filter_data() to filter out low-quality cells and genes - Added calculate_qc_metrics() to compute mitochondrial gene percentages and other QC stats - Added select_highly_variable_genes() to identify informative genes for downstream analysis These reusable functions improve code clarity and support scalable single-cell preprocessing workflows.
…ly_variable_genes Feature/filtering qc metrics highly variable genes
Feature/oop modules
Revert "Feature/oop modules"
3 functions are added to my new branch named issue_43
Ready for review: Implemented core user authentication (registration, login, password reset) and integrated with PostgreSQL.
Gene filtering
…tering Feature/computing embedding clustering
Last pca process
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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Outdated suggestions cannot be applied.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.
PR: Add plotting functions for scRNA-seq data
Description
This PR introduces four plotting utility functions for single-cell RNA-seq data:
pca_plot()highvarGen_pl()violin_pl()scatter_plotting()These functions are now located in
modules/plotting_utils.pyand are designed to enhance modularity and prevent cluttering the main project directory.Tools Used
scanpymatplotlibAll plots include basic error handling with
raise ValueErrorif required data (e.g.,"Cell type") is missing inadata.obs.Demo Output
Violin Plot Example Output