Rename cluster to addCluster #502
Conversation
fix identation
Merge branch 'master' of https://github.com/microbiome/mia into rename_cluster # Conflicts: # R/deprecate.R # man/deprecate.Rd
Merge branch 'master' of https://github.com/microbiome/mia into rename_cluster # Conflicts: # R/cluster.R # tests/testthat/test-9cluster.R
Merge branch 'master' of https://github.com/microbiome/mia into rename_cluster # Conflicts: # NEWS
R/deprecate.R
Outdated
| #' @param x A | ||
| #' \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment}} | ||
| #' object. | ||
| #' | ||
| #' @param clust.col A single character value indicating the name of the | ||
| #' \code{rowData} (or \code{colData}) where the data will be stored. | ||
| #' | ||
| #' @param exprs_values a single \code{character} value for specifying which | ||
| #' assay to use for calculation. | ||
| #' (Please use \code{assay.type} instead.) | ||
| #' | ||
| #' @param transposed Logical scalar, is x transposed with cells in rows? | ||
| #' | ||
| #' @param type the type of measure used for the goodness of fit. One of |
There was a problem hiding this comment.
This manual page should collect all deprecated functions. Some of them might have same parameter name but different meaning. So I'm wondering what happens then. --> I'm wondering if it is better to not list parameters for any of these functions since user's should not use them anyways (even though BIocCheck would tell otherwise)
R/deprecate.R
Outdated
| name = "clusters", clust.col = "clusters", ...){ | ||
| .Deprecated(msg = paste0("'cluster' is deprecated. ", | ||
| "Use 'addCluster' instead.")) | ||
| addCluster(x) |
There was a problem hiding this comment.
This does not pass parameters. addCluster gets only x parameter. Not others. Moreover, you can skip listing parameters. Use ... and then pass them to addCluster with ...
Only x is needed to list since the method is chosen based on class of x
There was a problem hiding this comment.
The idea is to keep these functions a hollow as possible. Just that they work but do not do anything but call the new function
R/calculateDMM.R
Outdated
| setMethod("calculateDMN", signature = c(x = "SummarizedExperiment"), | ||
| function(x, assay.type = assay_name, assay_name = exprs_values, exprs_values = "counts", | ||
| transposed = FALSE, ...){ | ||
| .Deprecated(old="calculateDMN", new="cluster", | ||
| "Now calculateDMN is deprecated. Use cluster with DMMParam parameter instead.") | ||
| mat <- assay(x, assay.type) | ||
| if(!transposed){ | ||
| mat <- t(mat) | ||
| } | ||
| calculateDMN(mat, ...) | ||
| } | ||
| function(x, assay.type = assay_name, assay_name = exprs_values, exprs_values = "counts", | ||
| transposed = FALSE, ...){ | ||
| .Deprecated(old="calculateDMN", new="cluster", | ||
| "Now calculateDMN is deprecated. Use cluster with DMMParam parameter instead.") | ||
| mat <- assay(x, assay.type) | ||
| if(!transposed){ | ||
| mat <- t(mat) | ||
| } | ||
| calculateDMN(mat, ...) | ||
| } | ||
| ) | ||
|
|
There was a problem hiding this comment.
It seems that the indentation is incorrect. Also lines are too long (80 characters is maximum)
Can you either fix these or revert the file? Maybe remove the changes, since this PR is about cluster function
Otherwise, this is ready to go. Thanks!
|
There are unresolved comments, and one conflict. If those are resolved then this seems good to me at least? |
Merge branch 'devel' of https://github.com/microbiome/mia into rename_cluster # Conflicts: # NEWS
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## devel #502 +/- ##
==========================================
- Coverage 73.11% 72.90% -0.21%
==========================================
Files 40 40
Lines 4630 4643 +13
==========================================
Hits 3385 3385
- Misses 1245 1258 +13 ☔ View full report in Codecov by Sentry. |
Rename
clustertoaddCluster.Fix indentation in calculateDMM and cluster files following Bioconductor best practices (indentation must be a multiple of 4 spaces).
Move deprecated functions from the calculateDMM file to deprecate file.