SIAMCAT issueshttps://git.embl.de/grp-zeller/SIAMCAT/-/issues2019-01-02T12:40:01Zhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/1finalizing mlr integration2019-01-02T12:40:01ZKonrad Zychfinalizing mlr integration- [x] extend support for more methods
- [x] generic retrieval methods for elements from the model
- [x] full integration of evaluation- [x] extend support for more methods
- [x] generic retrieval methods for elements from the model
- [x] full integration of evaluationVersion 0.3.0Konrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/2Update roxygen documentation2019-01-09T12:17:36ZKonrad ZychUpdate roxygen documentationBioconductor submissionJakob WirbelJakob Wirbelhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/3Mastering the issues2019-04-08T11:12:21ZKonrad ZychMastering the issues- [x] adding all the urgent TODO items as a separated issues and assign them to correct milestones
- [x] referencing them in relevant comments (see: https://about.gitlab.com/2016/03/08/gitlab-tutorial-its-all-connected/)
- [x] adding as ...- [x] adding all the urgent TODO items as a separated issues and assign them to correct milestones
- [x] referencing them in relevant comments (see: https://about.gitlab.com/2016/03/08/gitlab-tutorial-its-all-connected/)
- [x] adding as issues all the core functions that read/write data from the diskNijmegen conferenceJakob WirbelJakob Wirbelhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/4Splitting the core_functions file2017-09-28T09:58:42ZKonrad ZychSplitting the core_functions filesplitting this one massive file :shit: into separated files:
1. each core functions goes to a separated file
2. file name is the name of the function
3. all relevant utils are moved to the new function file from the terrible util files :...splitting this one massive file :shit: into separated files:
1. each core functions goes to a separated file
2. file name is the name of the function
3. all relevant utils are moved to the new function file from the terrible util files :poop:
4. everyting is awesome :cool: :sunglasses: :sunglasses: :sunglasses:Nijmegen conferenceJakob WirbelJakob Wirbelhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/7Update data.splitter()2017-09-28T11:52:23ZJakob WirbelUpdate data.splitter()- [x] delete/work on `inseparable` parameter
- [x] delete `meta` parameter
- provide default values?- [x] delete/work on `inseparable` parameter
- [x] delete `meta` parameter
- provide default values?Nijmegen conferencehttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/8Update documentation for eval.result()2017-09-29T14:55:28ZJakob WirbelUpdate documentation for eval.result()Nijmegen conferenceJakob WirbelJakob Wirbelhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/11Update documentation2018-03-30T07:45:18ZJakob WirbelUpdate documentationUpdate documentation in all the functions after the `siamcat-class` introduction
- [x] `add.meta.pred`
- [x] `check.associations`
- [x] `check.confounders`
- [x] `create.data.split`
- [x] `evaluate.predictions`
- [x] `filter.features`
-...Update documentation in all the functions after the `siamcat-class` introduction
- [x] `add.meta.pred`
- [x] `check.associations`
- [x] `check.confounders`
- [x] `create.data.split`
- [x] `evaluate.predictions`
- [x] `filter.features`
- [x] IO-utils functions
- [x] `make.predictions`
- [x] `model.evaluation.plot`
- [x] `model.interpretation.plot`
- [x] `normalize.features`
- [x] `select.samples`
- [ ] `siamcat.class` and accompanying functions
- [x] `train.model`
- [x] `validate.data`
Bioconductor submissionKonrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/13Update how plm.trainer takes in the training instances2017-09-28T11:52:47ZJakob WirbelUpdate how plm.trainer takes in the training instancesCurrently, the training instance indices have to be supplied to plm.trainer as file. Should be adjusted so that the function does not read/write data to diskCurrently, the training instance indices have to be supplied to plm.trainer as file. Should be adjusted so that the function does not read/write data to diskNijmegen conferencehttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/14Update plm.trainer()2018-01-16T13:40:24ZJakob WirbelUpdate plm.trainer()- [x] implement modsel.criterion
- [x] implement model.type as parameter- [x] implement modsel.criterion
- [x] implement model.type as parameterBioconductor submissionKonrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/15Update how plm.predictor takes in the test data2017-10-02T11:04:33ZJakob WirbelUpdate how plm.predictor takes in the test dataCurrently, plm.predict takes a set of features and labels as test data.
But it would be better if it could, analogously to plm.trainer, take the list returned by data.splitter as inputCurrently, plm.predict takes a set of features and labels as test data.
But it would be better if it could, analogously to plm.trainer, take the list returned by data.splitter as inputNijmegen conferenceKonrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/17Taking care of the utils.R2017-09-28T11:51:24ZKonrad ZychTaking care of the utils.R- [x] removing all the :poop: `make_xyz_options` functions from the utils file
- [x] removing all the :poop: `make_xyz_options` functions from the R_script file
- [x] renaming it to read_data.R
- [x] add some docs for the read functions ...- [x] removing all the :poop: `make_xyz_options` functions from the utils file
- [x] removing all the :poop: `make_xyz_options` functions from the R_script file
- [x] renaming it to read_data.R
- [x] add some docs for the read functions (see Georg's readme and copy from there about file formats). Do not spend too much time here, once the structure is done there will be aconstructor function that would not expose any of those to the user!Nijmegen conferenceJakob WirbelJakob Wirbelhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/18Radical code clean-up fro metagenomics course2017-10-02T19:46:27ZKonrad ZychRadical code clean-up fro metagenomics course- [x] remove unused parameters
- [x] mlr only
- [x] add mlr-related parameters- [x] remove unused parameters
- [x] mlr only
- [x] add mlr-related parametersNijmegen conferenceKonrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/23Vignette2021-07-28T12:18:24ZKonrad ZychVignettewe need to write a full-Rmd vignette to acoompany the package on BioConductor (and also, because we want people to use the package) :smile: :smile_cat:we need to write a full-Rmd vignette to acoompany the package on BioConductor (and also, because we want people to use the package) :smile: :smile_cat:Bioconductor submissionhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/27Update galaxy interface2018-04-17T09:42:48ZKonrad ZychUpdate galaxy interface- [ ] incorporate latest version
- [ ] test
- [ ] :package: ship it- [ ] incorporate latest version
- [ ] test
- [ ] :package: ship itPublicationhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/32removing srcdir from R_script2018-01-16T13:39:42ZKonrad Zychremoving srcdir from R_scriptVersion 0.3.0Konrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/38Updating R_script2018-02-15T16:15:59ZKonrad ZychUpdating R_scriptTO match the siamcat data structure workflow.TO match the siamcat data structure workflow.Version 0.4.0Konrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/41Homogenous names2018-03-28T20:55:25ZKonrad ZychHomogenous names- [ ] class-siamcat slots are all using _ (data_split, otu_table)
- [ ] functions are using action.subject (split.data, plot.model.interpretation)
- [ ] SIAMCAT/R files names match name of the (main) function they contain
- [ ] plot. fun...- [ ] class-siamcat slots are all using _ (data_split, otu_table)
- [ ] functions are using action.subject (split.data, plot.model.interpretation)
- [ ] SIAMCAT/R files names match name of the (main) function they contain
- [ ] plot. functions are reserved namesBioconductor submissionKonrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/43Start using gitLab and issues system properly2018-04-17T09:40:13ZKonrad ZychStart using gitLab and issues system properly- [x] add, commit and push are your friends
- [ ] issues - make an issue for every problem/ bug you find, for every feature you are developing etc - make it verbose and easy to track for us
- [ ] be a pro and use Markdown and quick actio...- [x] add, commit and push are your friends
- [ ] issues - make an issue for every problem/ bug you find, for every feature you are developing etc - make it verbose and easy to track for us
- [ ] be a pro and use Markdown and quick actions (e.g. `/estimate` and `/spend`)
- [x] question authorityMorgan EssexMorgan Essexhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/45Bug in the interpretor.model.plot with heatmap.type="fc"2018-02-26T14:39:40ZKonrad ZychBug in the interpretor.model.plot with heatmap.type="fc"```
+++ preparing heatmap
NaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaN...```
+++ preparing heatmap
NaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs producedNaNs produced+++ plotting model properties
Layout height values: 0.1, 0.64, 0.26
+++ plotting titles
+++ plotting legend
Error in seq.default(round(min(img.data, na.rm = TRUE), digits = 1), round(max(img.data, :
'from' must be a finite number
```https://git.embl.de/grp-zeller/SIAMCAT/-/issues/48buggy test2018-02-27T13:01:33ZKonrad Zychbuggy testSummary
(Summarize the bug encountered concisely)
Relevant logs and/or screenshots
(Paste any relevant logs - please use code blocks (```) to format console output,
logs, and code as it's very hard to read otherwise.)
/cc @zychSummary
(Summarize the bug encountered concisely)
Relevant logs and/or screenshots
(Paste any relevant logs - please use code blocks (```) to format console output,
logs, and code as it's very hard to read otherwise.)
/cc @zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/49Adjust prediction function2018-03-14T08:52:39ZJakob WirbelAdjust prediction function### Summary
For proper hold-out testing, it would make sense for the `predict` function to be able to be given a new, unrelated dataset.
- [x] make option argument in predict function (another `siamcat` object)
- [x] if no hold-out dat...### Summary
For proper hold-out testing, it would make sense for the `predict` function to be able to be given a new, unrelated dataset.
- [x] make option argument in predict function (another `siamcat` object)
- [x] if no hold-out data are given, perform the function at it is now
- [x] if hold-out data are given, perform data sanity checks
- [x] apply model on hold-out data and return predictions
### Question
Should the function for the hold-out prediction return only the prediction matrix or a modified `siamcat` object?
### Affected functions/datasets/objects
- `make.predictions`
/cc @zychJakob WirbelJakob Wirbelhttps://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/53Accessors for SIAMCAT-class2018-03-30T07:45:00ZKonrad ZychAccessors for SIAMCAT-class### Summary
All slots in the class should be accessible by an accessor function
/cc @zych### Summary
All slots in the class should be accessible by an accessor function
/cc @zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/54Unit testing2018-04-16T11:34:55ZKonrad ZychUnit testing### Summary
Add unit testing to SIAMCAT with [testthat](http://testthat.r-lib.org/index.html)
### Useful link
http://bioconductor.org/developers/how-to/unitTesting-guidelines/
/cc @zych### Summary
Add unit testing to SIAMCAT with [testthat](http://testthat.r-lib.org/index.html)
### Useful link
http://bioconductor.org/developers/how-to/unitTesting-guidelines/
/cc @zychKonrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/56Vignette - how to get your data into SIAMCAT2018-05-23T13:51:02ZKonrad ZychVignette - how to get your data into SIAMCAT### Summary
A vignette that shows crucial steps in reading in and preprocessing your data to use in SIAMCAT
### Goals/sub-features
- [x] loading different data types with phyloseq
- [x] reading SIAMCAT type text files
- [x] adding phyl...### Summary
A vignette that shows crucial steps in reading in and preprocessing your data to use in SIAMCAT
### Goals/sub-features
- [x] loading different data types with phyloseq
- [x] reading SIAMCAT type text files
- [x] adding phyloseq-class object to siamcat-class object
/cc @zychBioconductor 1.0.1 releaseKonrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/57Change how label object is build2018-04-17T09:37:29ZKonrad ZychChange how label object is build### Summary
We need to use a scenario where an user is using phyloseq to read the data in and then the label is rebuild whilst creating phyloseq-class object from metadata.
### Goals/sub-features
- [x] a parameter which specifies which...### Summary
We need to use a scenario where an user is using phyloseq to read the data in and then the label is rebuild whilst creating phyloseq-class object from metadata.
### Goals/sub-features
- [x] a parameter which specifies which column of metadata should be used to create label
- [x] update siamcat constructor function
/cc @zych @jawirbelKonrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/58Use vapply instead of sapply and use seq_along and seq_len instead of 1:length2018-04-09T15:11:03ZKonrad ZychUse vapply instead of sapply and use seq_along and seq_len instead of 1:length- [ ] sapply -> vapply
- [ ] 1:n -> seqalong
- [ ] 1:length -> seq_len
/cc @zych @jawirbel- [ ] sapply -> vapply
- [ ] 1:n -> seqalong
- [ ] 1:length -> seq_len
/cc @zych @jawirbelBioconductor review 1https://git.embl.de/grp-zeller/SIAMCAT/-/issues/59Format the code better2018-04-17T09:25:30ZKonrad ZychFormat the code better### Summary
Format you code better, with formatR, and make the code more readable. Use 4 spaces instead of 2. The current formatting makes it hard to read your code. The 80 char limit needs to be reasonably followed as well. Important
...### Summary
Format you code better, with formatR, and make the code more readable. Use 4 spaces instead of 2. The current formatting makes it hard to read your code. The 80 char limit needs to be reasonably followed as well. Important
### Goals/sub-features
- [x] use formatR
- [x] 2 spaces -> 4 spaces
- [x] tabs -> 4 spaces
- [x] 80 char limit
- [x] multiples of 4 spaces for line indents
/cc @zych @jawirbelBioconductor review 1Konrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/60Use getter's and setter's for accessing slots in your class2018-04-16T07:35:39ZKonrad ZychUse getter's and setter's for accessing slots in your class- [x] use phyloseq accessors and assignment functions
### rebuild SIAMCAT object
This need to be done, otherwise we need accessors for each slot in each slot...
- [x] change data_split -> list
- [x] change label -> list
### change phy...- [x] use phyloseq accessors and assignment functions
### rebuild SIAMCAT object
This need to be done, otherwise we need accessors for each slot in each slot...
- [x] change data_split -> list
- [x] change label -> list
### change phyloseq slot name to physeq
In order to avoid mother of all name conflicts.
- [ ] <s>`siamcat@phyloseq` => `siamcat@physeq`</s>
- [x] `phyloseq<-` => `physeq<-`
- [x] `phyloseq()` => `physeq()`
### create assigment functions
- [x] `phyloseq<-`
- [x] `label<-`
- [x] `model_list<-`
- [x] `eval_data<-`
- [x] `norm_param<-`
- [x] `data_split<-`
- [x] `pred_matrix<-`
- [x] `orig_feat<-`
### correct accessors
- [x] generic slot accessor
- [x] `phyloseq()`
- [x] `otu_table()`
- [x] `label()`
- [x] `model_list()`
- [x] `eval_data()`
- [x] `norm_param()`
- [x] `data_split()`
- [x] `pred_matrix()`
- [x] `orig_feat()`
- [x] remove old ones when replaced
### eliminate @
- [x] correct accessors
- [x] use assigments in the returns of the functions
/cc @zych @jawirbelBioconductor review 1Konrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/61Use small helper function2018-04-18T11:13:31ZKonrad ZychUse small helper function### Summary
If you are copy pasting code, it can be made into a small helper function. There are many such examples throughout you codebase, these all need to be fixed.
`check_associations.r`
```
x.q = apply(data1, 1, function (x)q...### Summary
If you are copy pasting code, it can be made into a small helper function. There are many such examples throughout you codebase, these all need to be fixed.
`check_associations.r`
```
x.q = apply(data1, 1, function (x)quantile(x, c(0.05, 0.25, 0.5, 0.75, 0.95),
na.rm=TRUE, names=FALSE))
y.q = apply(data2, 1, function (x)quantile(x, c(0.05, 0.25, 0.5, 0.75, 0.95),
na.rm=TRUE, names=FALSE))
```
eg: modify your function to take in a quantiles vector too, and you can reuse it accross your entire package.
```
apply_quantile <- function(data, quantiles_vector) {
apply(data, 1,
function (x) quantile(x, quantiles_vector,
na.rm = TRUE, names = FALSE))
}
```
### Goals/sub-features
- [ ] find this replicated code
- [ ] replace with helper function
/cc @zych @jawirbelBioconductor review 1https://git.embl.de/grp-zeller/SIAMCAT/-/issues/62Take advantage of vectorized functions2018-04-18T11:13:22ZKonrad ZychTake advantage of vectorized functions### Summary
Take advantage of vectorized functions, like `rowMedians` and `colMedians` from the `matrixStats` package.
Also, take a look at `rowQuantiles` and `colQuantiles` from `matrixStats`. Avoid apply functions and loops and opt to...### Summary
Take advantage of vectorized functions, like `rowMedians` and `colMedians` from the `matrixStats` package.
Also, take a look at `rowQuantiles` and `colQuantiles` from `matrixStats`. Avoid apply functions and loops and opt to vectorize.
### Goals/sub-features
- [ ] identify
- [ ] apply
/cc @zych @jawirbelBioconductor review 1Jakob WirbelJakob Wirbelhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/63Remove commented out code.2018-04-05T20:10:36ZKonrad ZychRemove commented out code.Clear.
/cc @zychClear.
/cc @zychBioconductor review 1Jakob WirbelJakob Wirbelhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/64Remove nested for loops2018-04-18T11:13:14ZKonrad ZychRemove nested for loops- [ ] identify
- [ ] think :thinking:
- [ ] remove :bomb:
/cc @zych- [ ] identify
- [ ] think :thinking:
- [ ] remove :bomb:
/cc @zychBioconductor review 1https://git.embl.de/grp-zeller/SIAMCAT/-/issues/65Update DESCRIPTION2018-04-05T21:13:57ZKonrad ZychUpdate DESCRIPTION- [x] Just use Authors@R, there is no need of Author and Maintainer.
- [x] You can have only 1 maintainer
- [x] version bump
/cc @zych- [x] Just use Authors@R, there is no need of Author and Maintainer.
- [x] You can have only 1 maintainer
- [x] version bump
/cc @zychBioconductor review 1Konrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/66Use proper messaging2018-04-09T14:35:03ZJakob WirbelUse proper messagingInstead of `cat`, use `message` everywhere where applicable...Instead of `cat`, use `message` everywhere where applicable...https://git.embl.de/grp-zeller/SIAMCAT/-/issues/68Docs for internal functions2018-04-17T09:36:58ZKonrad ZychDocs for internal functions### Summary
We need to add docs for some of the internal functions.
We just need to be sure, but I think just `#' @keywords internal` should be enough. In that case some of those are safe already.
### Goals/sub-features
In `check_a...### Summary
We need to add docs for some of the internal functions.
We just need to be sure, but I think just `#' @keywords internal` should be enough. In that case some of those are safe already.
### Goals/sub-features
In `check_associations.r`:
- [x] associations.bean.plot
- [x] associations.box.plot
- [x] associations.quantile.box.plot
- [x] associations.quantile.rect.plot
- [x] associations.margins.plot
- [x] associations.aucs.plot
- [x] associations.fcs.plot
- [x] associations.pr.shift.plot
- [x] associations.pvals.plot
- [x] is.color
- [x] check.color.scheme
- [x] associations.labels.plot
- [x] analyse.binary.marker
- [x] change.transparency
- [x] quantiles.plot
- [x] create.tints
- [x] quantile.rect.plot
- [x] quantile.median.plot
In `evaluate_predictions.r`:
- [x] evaluate.classifier
- [x] evaluate.area.trapez
- [x] evaluate.get.pr
- [x] evaluate.calc.aupr
In `model_interpretation_plot.R`:
- [x] plot.feature.weights
- [x] plot.pred.and.meta
- [x] plot.proportion.of.weights
- [x] plot.percentage.of.features
- [x] plot.heatmap
- [x] prepare.heatmap.fc
- [x] prepare.heatmap.zscore
- [x] select.features
- [x] get.weights.matrix
In `plm_utils.R`:
- [x] train.plm
- [x] get.optimal.lambda.for.glmnet
- [x] get.parameters.from.param.set
In `siamcat_class_constructor.r`:
- [x] get.component.classes
- [x] is.component.class
In `train_model.r`:
- [x] measureAUPRC
/cc @zych @jawirbel Bioconductor review 1https://git.embl.de/grp-zeller/SIAMCAT/-/issues/85Bugs in check.associations2018-07-24T15:38:17ZKonrad ZychBugs in check.associations### Summary
- [x] the prevalence shift panel in the association checking is buggy (sth is wrong with the y coordinate of the bars)
- [x] the legend in the quantile.rect plot is also misplaced - especially its title…
- [x] the sort.by op...### Summary
- [x] the prevalence shift panel in the association checking is buggy (sth is wrong with the y coordinate of the bars)
- [x] the legend in the quantile.rect plot is also misplaced - especially its title…
- [x] the sort.by option is either misleading or doesn’t work “fc” doesn’t produce a sorting by fold change...
/cc @zych @jawirbelhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/86Bugs in read.features2018-09-20T12:50:54ZKonrad ZychBugs in read.features### Summary
- [x] the read.features function doesn’t understand an URL as fn.in.feat (while e.g. read.table does)
- [ ] pass on arguments to the underlying read.table function
- [ ] make the function more flexible
/cc @zych @jawirbel### Summary
- [x] the read.features function doesn’t understand an URL as fn.in.feat (while e.g. read.table does)
- [ ] pass on arguments to the underlying read.table function
- [ ] make the function more flexible
/cc @zych @jawirbelKonrad ZychKonrad Zychhttps://git.embl.de/grp-zeller/SIAMCAT/-/issues/87Bug in model.interpretation.plot2018-07-19T12:07:04ZKonrad ZychBug in model.interpretation.plot###Summary
- [ ] the metadata display in the model interpretation plot looks a bit strange in the sense that some rows are very light throughout due to the smaller range of values - some form of normalization (rescale every row to the in...###Summary
- [ ] the metadata display in the model interpretation plot looks a bit strange in the sense that some rows are very light throughout due to the smaller range of values - some form of normalization (rescale every row to the interval [-1, 1])
/cc @zych @jawirbelhttps://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 @jawirbelhttps://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/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/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/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/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/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 @jawirbel