SIAMCAT issueshttps://git.embl.de/grp-zeller/SIAMCAT/-/issues2020-01-31T14:43:09Zhttps://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 https://git.embl.de/grp-zeller/SIAMCAT/-/issues/95remove meta-column after construction the label in the constructor function2018-09-21T08:57:59ZJakob Wirbelremove meta-column after construction the label in the constructor function### Summary
throw out the column with the label (for plotting reasons later)
only in the constructor function, not the `create.label` function
### Affected functions/datasets/objects
`siamcat-constructor`
/cc @zych### Summary
throw out the column with the label (for plotting reasons later)
only in the constructor function, not the `create.label` function
### Affected functions/datasets/objects
`siamcat-constructor`
/cc @zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/94Store feature weights in SIAMCAT2018-08-16T14:13:31ZJakob WirbelStore feature weights in SIAMCAT## Summary
Store mean/median feature weights in the slot for the models (for easier access, e.g. in `model.interpretation.plot`) and make them accessible by `model_weights(siamcat)` (or sth similar?)
## Affected functions/datasets/obj...## Summary
Store mean/median feature weights in the slot for the models (for easier access, e.g. in `model.interpretation.plot`) and make them accessible by `model_weights(siamcat)` (or sth similar?)
## Affected functions/datasets/objects
- `train.model`
- `model.interpretation.plot`
- `siamcat` Class
- `show` function
- accessors
- definition
/cc @zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/93Create tax table from appropriate feature names2018-08-13T06:57:52ZJakob WirbelCreate tax table from appropriate feature names## Summary
Create a tax table automatically from feature names that contain this information, i.e. k__;p__;g__ and so on
## Affected functions/datasets/objects
`summarize.features`
/cc @zych## Summary
Create a tax table automatically from feature names that contain this information, i.e. k__;p__;g__ and so on
## Affected functions/datasets/objects
`summarize.features`
/cc @zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/92easier label import2018-08-09T13:50:31ZJakob Wirbeleasier label importmake it possible to give a vector as label into the construction functionmake it possible to give a vector as label into the construction functionhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/91No NA handling in filter.features2018-08-09T13:52:14ZKonrad ZychNo NA handling in filter.features###Summary
If NAs are present in the data, the filter.features function does not work at all
###Relevant logs and/or screenshots
```
+ starting filter.features
+++ before filtering, the data has 1127 features
+++ applying abundance fi...###Summary
If NAs are present in the data, the filter.features function does not work at all
###Relevant logs and/or screenshots
```
+ starting filter.features
+++ before filtering, the data has 1127 features
+++ applying abundance filter
+++ checking for unmapped reads
+++ tried to remove unmapped reads, but could not find
them. Continue anyway.
+++ applying prune_taxa
+++ removed 1127 features whose values did not exceed 1e-04 in any sample (retaining 0)
Error in validObject(.Object) : invalid class "otu_table" object:
OTU abundance data must have non-zero dimensions.
```
/cc @zych @jawirbelKonrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/90clean the label class2018-08-01T14:14:26ZJakob Wirbelclean the label class- [x] remove redundant stuff in the label
- [x] fix all indexing calls with the label object- [x] remove redundant stuff in the label
- [x] fix all indexing calls with the label objecthttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/89fix constructor function2018-08-01T14:16:46ZJakob Wirbelfix constructor function- [x] use named arguments
- [x] perform some checks on features/labels/metadata
- [x] call data validator at the end of the constructor
- [x] SIAMCAT without the label (or NaN label)- [x] use named arguments
- [x] perform some checks on features/labels/metadata
- [x] call data validator at the end of the constructor
- [x] SIAMCAT without the label (or NaN label)Konrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/88bug in evaluate.predictions for models without resampling2018-07-19T13:36:17ZJakob Wirbelbug in evaluate.predictions for models without resampling### Summary
if no resampling has been performed (and thus the prediction is a single vector), the evaluation is buggy
### Relevant logs and/or screenshots
```
> + finished evaluate.predictions in 5.15 s
> Warning message:
> In pr[1]...### Summary
if no resampling has been performed (and thus the prediction is a single vector), the evaluation is buggy
### Relevant logs and/or screenshots
```
> + finished evaluate.predictions in 5.15 s
> Warning message:
> In pr[1] <- list(evaluate.get.pr(ev[[1]]), verbose = verbose) :
> number of items to replace is not a multiple of replacement length
```
/cc @zych @jawirbel