2.0.2

MetaR has been migrated to MPS 3.4.

2.0.0

• Support for instant refresh for both Analysis and composable R scripts.
• Support for MetaR results inside composable R. This makes it possible to view plots directly embedded in a composable R script. In essence this is a first step towards a fully composable electronic notebook where both results and output are mingled in an editor.
  Instant refresh now runs scripts directly without Jupyter. This improves speed of refreshes and makes it possible to execute with either a local R installation or the docker container support already offered by MetaR.
• Preliminary support for detecting minimal set of code changes to execute to refresh the analysis.
• Many editing bugs have been fixed to make Composable R easier to edit.
• Fluent parsing issues were fixed, resulting in improved experience when entering R code.
• Support for the magritte and diplyr operators, as well as the complete set of R user operators. You can now write dplyr code directly in composable R.

1.9.0

• First draft release of instant refresh feature. This feature detects changes made in analysis and rerun the analysis using a
• Jupyter notebook running in a docker container. Results returned by the execution are displayed directly in the analysis as they are returned. Developed by Alexander Pann.
• Improved refreshing of images and tables when the result file changes.
• Language metar.r.access provides access to MetaR tables and columns from composable R and is now included in R devkit for easier discoverability (these concepts were previously packaged in the BiomartToR language).
• Added empty line in R expressions in MetaR constructor. Previously, fluent parsing did not work because the R expressions were initially empty.

1.8.0.1

• Add ability to resize gene name labels, using the GeneNameSize style item.
• MAPlot: fix a number of problems. For instance: fix a bug that prevented the annotation of gene names when the gene name was identified with a column group other than ID.
• Substantially improve editing experience for multiplot.
• Composable R: Add actions to convert a OP b into a or b if one of the operands is deleted. This help edit code that uses operators more fluently.
• Composable R: add intention to quote a column name, i.e., transform table$col into table$”col”.
• Composable R: Improve R editing for parameter values. Make it possible to type a comma before a parameter and add a parameter at the beginning of the parameter list. Fix some problems deleting parameters.
• Propagate catch error in DrawPlot.
• Join table statement: call the correct rename function from plyr, even when dplyr hides it with another function also called rename. This resolves #6
• Eliminate console output when using histogram.
• Biomart: Quote column that match group ID. This resolves #2
• Resolved issue #5

1.8.0 April 15 2016

• Add normalized table output for Limma Voom statement (previously normalized counts were written to the adjusted table, but this table was only available if you had more than one factor in the model). This change makes it possible to get normalized expression data in the more common situation of a model with one factor.
• Add the ability to choose a group to identify the column that contains the names of the genes to show on a heatmap.
• Migration script will set this new annotation to the default ID group.
• Add support to generate MA Plots as well as UpSet plots
• Add support for Sleuth. You can now read Kallisto results directly with MetaR and call transcripts differentially expressed with Sleuth. The sleuth statement integrates with the Table annotation capabilities of MetaR and supports both Wald and likelihood ratio tests.
• Improve editing of R code, especially when calling functions.
• Change the keystroke to open the table viewer. It was bound to Shift T, which prevented users from typing an uppercase T in the table name.
• Code: started using the org.campagnelab.metar.R language to write generators for MetaR statements. Added metar.R.inspect to help with development of generators using the R language (this language is the equivalent of the metar.inspect language which was designed to be used with TextOutput in generators).
  *Code: Add IListenOnPort ConceptInterface and use it when ports need to be exposed by docker when executing a script.

Version described in the MetaR manuscript

This release contains the code described in our manuscript: http://biorxiv.org/content/early/2015/11/04/030254