Merge pull request #33 from microbiome/bioreview

Implement Bioconductor feedback

DESCRIPTION

@@ -14,7 +14,7 @@ Description:
     visualisation to create panels that are specific for
     TreeSummarizedExperiment objects. Not surprisingly, it also depends on the
     generic panels from iSEE.
-biocViews: Microbiome, Software, Visualization, DataImport
+biocViews: Microbiome, Software, Visualization, GUI, ShinyApps
 License: Artistic-2.0
 Encoding: UTF-8
 Depends:

R/class-AbundanceDensityPlot.R

@@ -32,9 +32,14 @@
 #' # Add relabundance assay
 #' tse <- transformAssay(tse, method = "relabundance")
 #'
-#' # Launch iSEE
+#' # Store panel into object
+#' panel <- AbundanceDensityPlot()
+#' # View some adjustable parameters
+#' head(slotNames(panel))
+#'
+#' # Launch iSEE with custom initial panel
 #' if (interactive()) {
-#'   iSEE(tse)
+#'   iSEE(tse, initial = c(panel))
 #' }
 #' 
 #' @docType methods

R/class-AbundancePlot.R

@@ -27,9 +27,14 @@
 #' data("Tengeler2020", package = "mia")
 #' tse <- Tengeler2020
 #' 
-#' # Launch iSEE
+#' # Store panel into object
+#' panel <- AbundancePlot()
+#' # View some adjustable parameters
+#' head(slotNames(panel))
+#' 
+#' # Launch iSEE with custom initial panel
 #' if (interactive()) {
-#'   iSEE(tse)
+#'   iSEE(tse, initial = c(panel))
 #' }
 #' 
 #' @docType methods

R/class-RDAPlot.R

@@ -50,9 +50,14 @@
 #'               distance = "bray",
 #'               na.action = na.exclude)
 #'
-#' # Launch iSEE with custom initial panels
+#' # Store panel into object
+#' panel <- RDAPlot()
+#' # View some adjustable parameters
+#' head(slotNames(panel))
+#'
+#' # Launch iSEE with custom initial panel
 #' if (interactive()) {
-#'   iSEE(tse, initial = c(RDAPlot()))
+#'   iSEE(tse, initial = c(panel))
 #' }
 #' 
 #' #' @docType methods

R/class-RowTreePlot.R

@@ -46,9 +46,14 @@
 #' data("Tengeler2020", package = "mia")
 #' tse <- Tengeler2020
 #' 
-#' # Launch iSEE
+#' # Store panel into object
+#' panel <- RowTreePlot()
+#' # View some adjustable parameters
+#' head(slotNames(panel))
+#'
+#' # Launch iSEE with custom initial panel
 #' if (interactive()) {
-#'   iSEE(tse)
+#'   iSEE(tse, initial = c(panel))
 #' }
 #' 
 #' @docType methods

R/iSEE-default.R

@@ -3,11 +3,13 @@
 #' Panel configuration tuned to the specific properties of
 #' \code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-constructor]{TreeSummarizedExperiment}}.
 #' 
+#' @inherit iSEE::iSEE params details sections
+#' 
 #' @return
 #' The iSEE method for the TreeSE container returns a default set of panels
 #' typically relevant for microbiome data. This configuration can be modified
-#' by defining a different set of initial panels. By default, the visualised
-#' panels include the following:
+#' by defining a different set of initial panels. By default, the interface
+#' includes the following panels:
 #' \itemize{
 #' \item \code{RowDataTable()}
 #' \item \code{ColumnDataTable()}
@@ -38,12 +40,11 @@
 #' }
 #' 
 #' @docType methods
-#' @aliases iSEE
-#'   iSEE,TreeSummarizedExperiment-method
-#'
-#' @name iSEE-default
+#' @aliases iSEE,TreeSummarizedExperiment-method
+#' @name iSEE
 NULL
 
+#' @rdname iSEE
 #' @export
 setGeneric("iSEE", iSEE::iSEE)
 

README.md

@@ -11,13 +11,27 @@ objects which facilitate the interactive visualisation of microbiome data in
 [_iSEE_](https://isee.github.io/).
 
 ## Installation instructions
-The development version of iSEEtree can be installed from GitHub as follow:
+The release version of iSEEtree can be installed from Bioconductor as follows:
 
 ```
-remotes::install_github("microbiome/iSEEtree")
+if (!requireNamespace("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+
+BiocManager::install("iSEEtree")
+```
+
+Contributors or users interested in the latest functionality can install the
+devel version of iSEEtree as follows:
+
 ```
+if (!requireNamespace("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+
+# The following initializes usage of Bioc devel
+BiocManager::install(version='devel')
 
-In the future, this package may be submitted to Bioconductor.
+BiocManager::install("mia")
+```
 
 ## Example
 The basic functionality of iSEEtree can be explored as follows:
@@ -70,8 +84,7 @@ This package was developed using
 ## Code of Conduct
 Please note that the iSEEtree project is released with a
 [Contributor Code of Conduct](https://bioconductor.org/about/code-of-conduct/).
-By contributing to this project, you agree to abide by its terms. If you come
-across a bug or see potential for improvement, feel free to open an issue and we
-will plan the next move. is missing or could be improved. If you are interested
-in contributing, you can check [our issues](https://github.com/microbiome/iSEEtree/issues)
-and try to find a solution. Either way, contributions are very much appreciated.
+By contributing to this project, you agree to abide by its terms. Contributions
+are welcome in the form of feedback, issues and pull requests. You can find the
+contributor guidelines of the miaverse
+[here](https://github.com/microbiome/mia/blob/devel/CONTRIBUTING.md).