Upgrade altair v5 #56
Open
Conversation
This file contains 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
…he latest version of altair available through Anaconda, and Qiime 2's latest env files are installing altair v5.0.1.
…ion was deprecated in altair v5, and changed to selection_point(). Also changed add_selection(), in repScatters() when charts are being put together, since funciton was also deprecated in altair v5, and changed to add_params(). Added TODO comments in places in mutantScatters() where deprecated functions also need to be changed.
…selection_single". Changed line 350 in zenrich.py to call "selection_point" instead of "selection_single". This is because "selection_single" has been deprecated, so calling replacement/new functions reduces work in the future when deprecated functions are removed.
…rich functions. Need to take care of other TODO comments where I did not change calls yet.
…" in heatmap.py and zenrich.py to "add_params" since the aforementioned is now deprecated.
…ar to calls in other files.
…th' parameter to fit what the parameter actually means/does.
…EA. Still need to implement a highlighted probes graph for leading edge genes. Lastly, will be to reformat zenrich to handle both diffEnrich and PSEA.
…nt in the Z score scatter plot.
…ing genes to visualizatio.
… the genes which were identified as "lead genes", as well as has a curve for the spline operation carried out for the residuals.
…s to figure out the appropriate type for 'p_vals' and 'es' parameters.
… where Qiime2 would complain about not being able to determine a constructor for a tag related to numpy.core.multiarray.scalar.
…be taxa with p-values and es's above those specified by the user.
…ment significan taxa highlighting for the Z score scatter plot.
… on the taxa to which they belong.
… maps taxa to their leading edge peptides identified by PSEA. This format makes highlighting leading edge peptides based on the taxa to which they belong easier.
… compared the absolute value of enrichment score to the enrichment score threshold: allows for highlighting of strongly negative and positive enrichment scores.
…a single legend for mark shape and colors. Volcano plot now takes the log of passed p-values and plots those, and compares non-transformed p-values to the threshold to identify points to highlight.
…facilitate a more general use case.
…enrich_tsv after moving scatter plot code into a separate function. Made some last minute changes to volcano function.
Created "include species" option for proteinHeatmap-dir pipeline
…what is shown in the legend on the volcano plot.
Psea plots
…odulo operator in zscatter and volcano functions, respectively. This accounts for when the user passes a single value to the parameters.
… the volcano plot share shape and color with highlighted points in scatter plot.
Psea plots
…and other visualization options. Call using 'qiime ps-plot epimap-dir'
Upgrade altair v5
…zscore differece and pval information for each peptide. I also temporily removd the use of the chart making function in heatmap and epimap as it is still being developed.
Epimap changes
…till baring the ability to render.
…Unfortunately, the points are back to extending outside the extents of the chart.
…ne in zenrich does not map the points into the chart. Added more intuitive axis labels.
…nges to 'y_thresholds' and 'highlight_thresholds' parameters since we are no longer manually adjusting the p-value threshold after running PSEA.
…hlight data if they do not have/wish to have species highlighted. Additionally, made zscatter() and volcano() more general so a parameter is used to choose which names are used to highlight. This allows for the use of taxa IDs instead of species names, if that data is not available.
Adding drop down
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.
Update main to Altair version 5. I created a release to preserve the code for Altair version 4