SIAMCAT issueshttps://git.embl.de/grp-zeller/SIAMCAT/-/issues2018-04-23T12:06:02Zhttps://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/73Visualize ANOVA2018-07-10T07:28:55ZMorgan EssexVisualize ANOVA### Summary
Variance decomposition for each metadata variable
### Affected functions/datasets/objects
`check_associations_conf.r`
### Goals/sub-features
- [x] ANOVA on ranks for each metadata category
- [x] Implement Jakob's bubble p...### Summary
Variance decomposition for each metadata variable
### Affected functions/datasets/objects
`check_associations_conf.r`
### Goals/sub-features
- [x] ANOVA on ranks for each metadata category
- [x] Implement Jakob's bubble plots
- [x] Implement them in base
/cc @zychMorgan EssexMorgan Essexhttps://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/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/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/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/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 Zych