SIAMCAT issueshttps://git.embl.de/grp-zeller/SIAMCAT/-/issues2022-02-16T09:46:50Zhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/29Code cleaning November2022-02-16T09:46:50ZKonrad ZychCode cleaning NovemberVersion 0.3.02017-11-30https://git.embl.de/grp-zeller/SIAMCAT/-/issues/37Verbose2018-02-26T08:36:08ZKonrad ZychVerbose- make verbose an int argument in all the user-level function
- verbose>2 for debug-level information
- verbose>1 for info about functions running + some info about procesing
`if(verbose>1) cat("+ starting read.features\n")`
- verb...- make verbose an int argument in all the user-level function
- verbose>2 for debug-level information
- verbose>1 for info about functions running + some info about procesing
`if(verbose>1) cat("+ starting read.features\n")`
- verbose>0: info that function did run + progress bars
`if(verbose>0) cat("+ finished read.features in",e.time-s.time,"s\n")`
- verbose==0 - nothing
Should be done for these functions:
- [x] `add.meta.pred`
- [x] `check.associations`
- [x] `check.confounders`
- [x] `eval.predictions`
- [x] `filter.feat`
- [x] `normalize.feat`
- [ ] `plot.model.evaluation`
- [ ] `plot.model.interpretation`
- [x] `make.predictions`
- [x] `select.samples`
- [x] `data.splitter`
- [x] `train.model`
Version 0.4.0Konrad ZychKonrad Zych2018-02-23https://git.embl.de/grp-zeller/SIAMCAT/-/issues/52Bioconductor submission checklist2018-03-30T07:44:52ZKonrad ZychBioconductor submission checklist- [x] clone to GitHub/ check if it could be submitted from git.embl
- [x] R CMD check with no warnings and errors
- [x] R CMD BiocCheck with no warnings and errors
- [x] R CMD BiocCheck notes - careful with those
- [x] siamcat_example do...- [x] clone to GitHub/ check if it could be submitted from git.embl
- [x] R CMD check with no warnings and errors
- [x] R CMD BiocCheck with no warnings and errors
- [x] R CMD BiocCheck notes - careful with those
- [x] siamcat_example does not work with log.std normalization
- [x] replacing previous import ‘mlr::auc’ by ‘pROC::auc’ when loading ‘SIAMCAT -> importsFrom should solve it but seems not to work properly?
- [x] The result of R CMD build must be less than 4MB
- [x] R CMD check must complete within 5 minutes
- [x] Set Version: 0.99.0 in the DESCRIPTION
- [x] Include an inst/NEWS file for providing users with information on package updates
- [ ] NOTE: Consider shorter lines
- [ ] NOTE: Consider multiples of 4 spaces for line indentsBioconductor submission2018-03-29https://git.embl.de/grp-zeller/SIAMCAT/-/issues/70Bipartite network graph for metadata & feature visualization2018-04-23T12:06:02ZMorgan EssexBipartite network graph for metadata & feature visualization### Summary
High-level intro graph for confounder association module to quickly visualize associations between confounders and metadata.
Using igraph package.
### Affected functions/datasets/objects
TBA confounder branch
### Goals/su...### Summary
High-level intro graph for confounder association module to quickly visualize associations between confounders and metadata.
Using igraph package.
### Affected functions/datasets/objects
TBA confounder branch
### Goals/sub-features
- [x] feature nodes scaled and/or colored according to label association (metadata nodes?)
- [x] edges scaled and/or colored according to Kruskal-Wallis test p-values for each metadata category
- [x] overlay with mtext or sth for labels? (igraph labels are terrible)
/cc @zychMorgan EssexMorgan Essex2018-04-20https://git.embl.de/grp-zeller/SIAMCAT/-/issues/72Legends for network graph2018-04-23T14:59:37ZMorgan EssexLegends for network graph### Summary
Adding legend/small details to network graph for confounder associations
### Affected functions/datasets/objects
TBA confounder brance
### Goals/sub-features
- [x] legend for node colors
- [x] legend for edge colors
/c...### Summary
Adding legend/small details to network graph for confounder associations
### Affected functions/datasets/objects
TBA confounder brance
### Goals/sub-features
- [x] legend for node colors
- [x] legend for edge colors
/cc @zychMorgan EssexMorgan Essex2018-04-24https://git.embl.de/grp-zeller/SIAMCAT/-/issues/74Metadata GLMs2018-04-30T21:34:22ZMorgan EssexMetadata GLMs### Summary
Simple glms for each metadata
### Affected functions/datasets/objects
check_confounders.r
### Goals/sub-features
- [x] glms
- [x] au-rocs
- [x] correlation with label (and one another?? later...)
/cc @zych### Summary
Simple glms for each metadata
### Affected functions/datasets/objects
check_confounders.r
### Goals/sub-features
- [x] glms
- [x] au-rocs
- [x] correlation with label (and one another?? later...)
/cc @zychMorgan EssexMorgan Essex2018-05-02https://git.embl.de/grp-zeller/SIAMCAT/-/issues/71Visualize blocking results2018-05-16T19:49:27ZMorgan EssexVisualize blocking results### Summary
Adjusted p value plot (stacked lines or bars?) to show blocking results for top 5 metadata
### Affected functions/datasets/objects
`check_associations_conf.r`
/cc @zych### Summary
Adjusted p value plot (stacked lines or bars?) to show blocking results for top 5 metadata
### Affected functions/datasets/objects
`check_associations_conf.r`
/cc @zychMorgan EssexMorgan Essex2018-05-09https://git.embl.de/grp-zeller/SIAMCAT/-/issues/75Base bipartite intro map2018-05-11T07:42:55ZMorgan EssexBase bipartite intro map### Summary
Remove igraph dependencies in favor of base graphics for intro visualization in confounder association check module
### Affected functions/datasets/objects
TBA Confounder module
Currently just my isolated script
### Goals...### Summary
Remove igraph dependencies in favor of base graphics for intro visualization in confounder association check module
### Affected functions/datasets/objects
TBA Confounder module
Currently just my isolated script
### Goals / sub-features
- [x] for metadata (confounder_check)
- [x] for features (associations_conf_check)
/cc @zychMorgan EssexMorgan Essex2018-05-10https://git.embl.de/grp-zeller/SIAMCAT/-/issues/107parameter for `evaluation.plot`2020-01-31T14:43:09ZJakob Wirbelparameter for `evaluation.plot`parameter to turn off ROC curves from individual cross-validation runsparameter to turn off ROC curves from individual cross-validation runsJakob WirbelJakob Wirbelhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/106Feature request: warning if the species are too long to fit on the associatio...2019-11-01T11:35:46ZJakob WirbelFeature request: warning if the species are too long to fit on the association plotpretty well described in the title...pretty well described in the title...https://git.embl.de/grp-zeller/SIAMCAT/-/issues/105special characters in label names are removed2019-10-14T12:16:10ZJakob Wirbelspecial characters in label names are removedspecial characters in label names are removed, so that the names will be the same if you use `(1, -1)` as labelsspecial characters in label names are removed, so that the names will be the same if you use `(1, -1)` as labelsJakob WirbelJakob Wirbelhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/104include feature weights in the models slot of the siamcat object?2019-09-17T14:15:25ZJakob Wirbelinclude feature weights in the models slot of the siamcat object?include the feature weights and weights table in different slots in the models slot of the siamcat object for easier access
for models trained on gene group abundance data, the retrieval of feature weights takes forever and could be spe...include the feature weights and weights table in different slots in the models slot of the siamcat object for easier access
for models trained on gene group abundance data, the retrieval of feature weights takes forever and could be sped up by saving the tables directlyJakob WirbelJakob Wirbelhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/103some minor issues with the multiple hypothesis testing in check.associations2019-10-14T12:16:01ZJakob Wirbelsome minor issues with the multiple hypothesis testing in check.associationsin `check.associations`, there are two adjustments to be made:
- allowed multiple hypothesis correction methods do not overlap with the allowed ones in `p.adjust`
- if no correction is performed, the plot should NOT say adj. p value in t...in `check.associations`, there are two adjustments to be made:
- allowed multiple hypothesis correction methods do not overlap with the allowed ones in `p.adjust`
- if no correction is performed, the plot should NOT say adj. p value in the x axisJakob WirbelJakob Wirbelhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/102NEWS for Release 3.92019-04-25T09:03:08ZKonrad ZychNEWS for Release 3.9* Bugfix for add.meta.pred function
* Bugfix for confounder-check function
* Included vignette figures in man/figure
* Bugfix for summarize.features function
* Bugfix for siamcat creator function
* Fixed centered log ratio transform to b...* Bugfix for add.meta.pred function
* Bugfix for confounder-check function
* Included vignette figures in man/figure
* Bugfix for summarize.features function
* Bugfix for siamcat creator function
* Fixed centered log ratio transform to be per sample and not per feature
/cc @jawirbel @zeller @zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/101Feature request for check.associations2019-02-07T10:33:49ZKonrad ZychFeature request for check.associationsadd an option to use paired=TRUE in `wilcox.test`
add an option to use paired=TRUE in `wilcox.test`
https://git.embl.de/grp-zeller/SIAMCAT/-/issues/100bug in evaluate.predictions()2019-01-09T12:24:28ZKonrad Zychbug in evaluate.predictions()###Summary
evaluate predictions fails when `num.resample = 1`
###Relevant logs and/or screenshots
```
+ starting evaluate.predictions
+ calculating ROC
|==============================================================================...###Summary
evaluate predictions fails when `num.resample = 1`
###Relevant logs and/or screenshots
```
+ starting evaluate.predictions
+ calculating ROC
|====================================================================================| 100%
+ starting evaluate.classifier
+ finished evaluate.classifier
+ starting evaluate.get.pr
+ finished evaluate.get.pr
+ starting evaluate.calc.aupr
+ starting evaluate.get.pr
+ finished evaluate.get.pr
+ finished evaluate.calc.aupr
+ evaluating single prediction
Error in validObject(.Object) :
invalid class “eval_data” object: Entry for roc is not an object of class roc (from pROC)!
```
/cc @zych @jawirbelhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/99Bug in siamcat() creator function2019-01-09T12:22:50ZKonrad ZychBug in siamcat() creator function###Summary
siamcat() will always fail when otu_table has taxa in columns (it assumes rows)
/cc @zych @jawirbel###Summary
siamcat() will always fail when otu_table has taxa in columns (it assumes rows)
/cc @zych @jawirbelKonrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/98Figure out how to take care of the Rscript flavor2018-10-01T19:16:47ZKonrad ZychFigure out how to take care of the Rscript flavorShould it stay out of the Bioconductor or should we add it?Should it stay out of the Bioconductor or should we add it?https://git.embl.de/grp-zeller/SIAMCAT/-/issues/97feature_weights/weight_matrix compute on the fly2018-09-07T11:33:41ZJakob Wirbelfeature_weights/weight_matrix compute on the fly### Summary
Instead of saving feature_weights/weight_matrix in the object, make the accessor functions compute them on the fly
### Affected functions/datasets/objects
`train.model`
`accessors`
/cc @zych### Summary
Instead of saving feature_weights/weight_matrix in the object, make the accessor functions compute them on the fly
### Affected functions/datasets/objects
`train.model`
`accessors`
/cc @zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/96on which type of features should the function work?2018-10-01T19:17:21ZJakob Wirbelon which type of features should the function work?### Summary
Include a parameter, on which type of features the function should work (i.e. original, filtered, normalized). Make smart defaults to keep the current workflow unaffected
### Affected functions/datasets/objects
- [x] `fil...### Summary
Include a parameter, on which type of features the function should work (i.e. original, filtered, normalized). Make smart defaults to keep the current workflow unaffected
### Affected functions/datasets/objects
- [x] `filter.features`
- [x] `normalize.features`
- [x] `check.associations`
- [x] `train.model`
- [x] `make.predictions`
- [x] `model.interpretation.plot`
- [x] `add.meta.pred`
- [x] `summarize.features`
/cc @zych @jawirbel