From 498cc529d6c3b198eae3d40cd0d97c0e5989cd81 Mon Sep 17 00:00:00 2001 From: Michael Steinbaugh Date: Thu, 5 Sep 2019 13:20:55 -0400 Subject: [PATCH 1/5] Specify pipeline in sample metadata load --- R/AllGenerators.R | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/R/AllGenerators.R b/R/AllGenerators.R index bd8e4fe1b..56fd31cc9 100644 --- a/R/AllGenerators.R +++ b/R/AllGenerators.R @@ -137,7 +137,11 @@ bcbioSingleCell <- function( allSamples <- TRUE sampleData <- NULL if (isString(sampleMetadataFile)) { - sampleData <- importSampleData(sampleMetadataFile, lanes = lanes) + sampleData <- importSampleData( + file = sampleMetadataFile, + lanes = lanes, + pipeline = "bcbio" + ) ## Error on incorrect reverse complement input. if ("sequence" %in% colnames(sampleData)) { sampleDirSequence <- str_extract(names(sampleDirs), "[ACGT]+$") From a9d849306af09f2c558f49e788a92736fd90bdd7 Mon Sep 17 00:00:00 2001 From: Michael Steinbaugh Date: Thu, 5 Sep 2019 16:58:05 -0400 Subject: [PATCH 2/5] Fix README --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 215392079..d3e3f0285 100644 --- a/README.md +++ b/README.md @@ -16,7 +16,7 @@ if (!requireNamespace("remotes", quietly = TRUE)) { } Sys.setenv(R_REMOTES_UPGRADE = "always") # Set `GITHUB_PAT` in `~/.Renviron` if you get a rate limit error. -remotes::install_github("hbc/bcbioRNASingleCell") +remotes::install_github("hbc/bcbioSingleCell") ``` Here's how to update to the latest version on GitHub: From c3fa3c4cf9522abbe840a910ba0e5e64c74169d6 Mon Sep 17 00:00:00 2001 From: Michael Steinbaugh Date: Mon, 9 Sep 2019 12:11:03 -0400 Subject: [PATCH 3/5] Update dependencies --- DESCRIPTION | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 3713e3af4..6562d2fa8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: bcbioSingleCell Title: bcbio Single-Cell RNA-Seq Description: R package for bcbio single-cell RNA-seq analysis. -Version: 0.4.3 -Date: 2018-08-27 +Version: 0.4.4 +Date: 2018-09-09 Authors@R: c( person( given = "Michael", @@ -54,12 +54,12 @@ LazyData: false Depends: R (>= 3.6), SingleCellExperiment (>= 1.6), - basejump (>= 0.11.11) + basejump (>= 0.11.14) Imports: acidplots (>= 0.2.14), bcbioBase (>= 0.6.10), - bioverbs (>= 0.2.7), - goalie (>= 0.3.6), + bioverbs (>= 0.2.9), + goalie (>= 0.3.7), BiocGenerics (>= 0.30), BiocParallel (>= 1.18), IRanges (>= 2.18.2), @@ -73,7 +73,7 @@ Imports: methods, utils Suggests: - acidroxygen (>= 0.1), + acidroxygen (>= 0.1.2), BiocStyle (>= 2.12), R.utils (>= 2.9), knitr (>= 1.24), From 890fe088a37d7f53ce9bf3db40b2ef60d47a8d8b Mon Sep 17 00:00:00 2001 From: Michael Steinbaugh Date: Mon, 9 Sep 2019 12:38:26 -0400 Subject: [PATCH 4/5] Rebuild website --- docs/404.html | 9 +- docs/CONTRIBUTING.html | 9 +- docs/LICENSE-text.html | 9 +- docs/authors.html | 9 +- docs/index.html | 184 ++++++++++---------- docs/news/index.html | 9 +- docs/news/news-0.1.html | 9 +- docs/news/news-0.2.html | 9 +- docs/news/news-0.3.html | 9 +- docs/news/news-0.4.html | 9 +- docs/pkgdown.css | 8 + docs/pkgdown.yml | 6 +- docs/reference/bcb.html | 20 +-- docs/reference/bcbioSingleCell-class.html | 19 +- docs/reference/bcbioSingleCell-package.html | 19 +- docs/reference/bcbioSingleCell.html | 39 ++--- docs/reference/bcbioSingleCellTestsURL.html | 18 +- docs/reference/defunct.html | 21 +-- docs/reference/deprecated.html | 21 +-- docs/reference/extract.html | 33 ++-- docs/reference/index.html | 9 +- docs/reference/plotReadsPerCell-1.png | Bin 85713 -> 52877 bytes docs/reference/plotReadsPerCell-2.png | Bin 70607 -> 42380 bytes docs/reference/plotReadsPerCell.html | 21 +-- docs/reference/reexports.html | 19 +- docs/reference/show.html | 25 +-- docs/reference/updateObject.html | 52 +++--- 27 files changed, 289 insertions(+), 306 deletions(-) diff --git a/docs/404.html b/docs/404.html index d50c9f10a..ffb45c593 100644 --- a/docs/404.html +++ b/docs/404.html @@ -8,11 +8,13 @@ Page not found (404) • bcbioSingleCell + + @@ -34,10 +36,12 @@ + + @@ -65,7 +69,7 @@ bcbioSingleCell - 0.4.3 + 0.4.4 @@ -84,7 +88,6 @@ Changelog - -
  • @@ -133,7 +136,7 @@

    -

    Site built with pkgdown 1.3.0.9100.

    +

    Site built with pkgdown 1.4.0.

    diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index d13518839..c5189f5a1 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -8,11 +8,13 @@ License • bcbioSingleCell + + @@ -34,10 +36,12 @@ + + @@ -65,7 +69,7 @@ bcbioSingleCell - 0.4.3 + 0.4.4 @@ -84,7 +88,6 @@ Changelog

- -
  • @@ -147,7 +150,7 @@

    Authors

    -

    Site built with pkgdown 1.3.0.9100.

    +

    Site built with pkgdown 1.4.0.

    diff --git a/docs/index.html b/docs/index.html index bfd8d00ef..a2713da36 100644 --- a/docs/index.html +++ b/docs/index.html @@ -32,7 +32,7 @@ bcbioSingleCell - 0.4.3 + 0.4.4 @@ -81,36 +81,36 @@

    R method

    -
    if (!requireNamespace("remotes", quietly = TRUE)) {
-    install.packages("remotes")
-}
-Sys.setenv(R_REMOTES_UPGRADE = "always")
-# Set `GITHUB_PAT` in `~/.Renviron` if you get a rate limit error.
-remotes::install_github("hbc/bcbioRNASingleCell")
    +
    if (!requireNamespace("remotes", quietly = TRUE)) {
+    install.packages("remotes")
+}
+Sys.setenv(R_REMOTES_UPGRADE = "always")
+# Set `GITHUB_PAT` in `~/.Renviron` if you get a rate limit error.
+remotes::install_github("hbc/bcbioSingleCell")

    Here’s how to update to the latest version on GitHub:

    -
    Sys.setenv(R_REMOTES_UPGRADE = "always")
-remotes::update_packages()
    +
    Sys.setenv(R_REMOTES_UPGRADE = "always")
+remotes::update_packages()

    Always check that your Bioconductor installation is valid before proceeding.

    -
    if (!requireNamespace("BiocManager", quietly = TRUE)) {
-    install.packages("BiocManager")
-}
-BiocManager::valid()
    +
    if (!requireNamespace("BiocManager", quietly = TRUE)) {
+    install.packages("BiocManager")
+}
+BiocManager::valid()

    Load bcbio single-cell RNA-seq data

    - +
    library(bcbioSingleCell)
+bcb <- bcbioSingleCell(
+    uploadDir = "indrops/final",
+    interestingGroups = c("genotype", "treatment"),
+    sampleMetadataFile = "sample_metadata.csv",
+    organism = "Homo sapiens",
+    ensemblRelease = 90L
+)
+saveData(bcb, dir = ".")

    This will return a bcbioSingleCell object, which is an extension of the Bioconductor SingleCellExperiment container class. Consult the bcbioSingleCell() constructor function documentation for detailed information on the supported parameters:

    -
    help(topic = "bcbioSingleCell", package = "bcbioSingleCell")
    +
    help(topic = "bcbioSingleCell", package = "bcbioSingleCell")

    @@ -123,77 +123,77 @@

    Consult the bcbio documentation for more information on how to configure an inDrops run prior to loading into R with the bcbioSingleCell() function.

    - - - - - - + + + + + + - - - - - - + + + + + + - - - - - - + + + + + + - - - - - - + + + + + + - - - - - - + + + + + + - - - - - - + + + + + + - - - - - - + + + + + + - - - - - - + + + + + + - - - - - - + + + + + +
    descriptionindexsequencesampleNameaggregategenotypedescriptionindexsequencesampleNameaggregategenotype
    indrops11CTCTCTATsample1_1sample1wildtypeindrops11CTCTCTATsample1_1sample1wildtype
    indrops12TATCCTCTsample2_1sample2knockoutindrops12TATCCTCTsample2_1sample2knockout
    indrops13GTAAGGAGsample3_1sample3wildtypeindrops13GTAAGGAGsample3_1sample3wildtype
    indrops14ACTGCATAsample4_1sample4knockoutindrops14ACTGCATAsample4_1sample4knockout
    indrops21CTCTCTATsample1_2sample1wildtypeindrops21CTCTCTATsample1_2sample1wildtype
    indrops22TATCCTCTsample1_2sample2knockoutindrops22TATCCTCTsample1_2sample2knockout
    indrops23GTAAGGAGsample1_2sample3wildtypeindrops23GTAAGGAGsample1_2sample3wildtype
    indrops24ACTGCATAsample1_2sample4knockoutindrops24ACTGCATAsample1_2sample4knockout
    @@ -205,25 +205,25 @@

    This is our current method for handling 10X Genomics Chromium and Illumina SureCell cell barcodes.

    - - + + - - + + - - + + - - + + - - + +
    descriptiongenotypedescriptiongenotype
    sample1wildtypesample1wildtype
    sample2knockoutsample2knockout
    sample3wildtypesample3wildtype
    sample4knockoutsample4knockout
    @@ -232,9 +232,9 @@

    Invalid object

    If you encounter a validObject error when attempting to load a bcbioSingleCell object from a previous analysis, run this step to update the object to the current version of the package:

    - +
    object <- updateObject(object)
+validObject(object)
+## [1] TRUE
    @@ -291,7 +291,7 @@

    Developers

    Dev status

    • Repo status: active
      • -
    • Travis CI build status
      • +
    • AppVeyor CI build status
    @@ -304,7 +304,7 @@

    Dev status

    -

    Site built with pkgdown 1.3.0.9100.

    +

    Site built with pkgdown 1.4.0.

    diff --git a/docs/news/index.html b/docs/news/index.html index 02af27e48..63989cd93 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -8,11 +8,13 @@ News • bcbioSingleCell + + @@ -34,10 +36,12 @@ + + @@ -65,7 +69,7 @@ bcbioSingleCell - 0.4.3 + 0.4.4 @@ -84,7 +88,6 @@ Changelog
- - - - -
  • @@ -197,7 +200,7 @@

    Contents

    -

    Site built with pkgdown 1.3.0.9100.

    +

    Site built with pkgdown 1.4.0.

    diff --git a/docs/pkgdown.css b/docs/pkgdown.css index 912cb8234..914595810 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -246,3 +246,11 @@ mark { .fab { font-family: "Font Awesome 5 Brands" !important; } + +/* don't display links in code chunks when printing */ +/* source: https://stackoverflow.com/a/10781533 */ +@media print { + code a:link:after, code a:visited:after { + content: ""; + } +} diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 9b00f0464..889d8136d 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,5 +1,5 @@ -pandoc: 2.3.1 -pkgdown: 1.3.0.9100 -pkgdown_sha: 1829398a4e97056fe7fb332d0e8b952784b49321 +pandoc: 1.12.3.1 +pkgdown: 1.4.0 +pkgdown_sha: ~ articles: [] diff --git a/docs/reference/bcb.html b/docs/reference/bcb.html index 28038690f..b27c6b36b 100644 --- a/docs/reference/bcb.html +++ b/docs/reference/bcb.html @@ -8,11 +8,13 @@ bcbio single-cell RNA-seq example data set — bcb • bcbioSingleCell + + @@ -34,13 +36,14 @@ - + + @@ -68,7 +71,7 @@ bcbioSingleCell - 0.4.3 + 0.4.4 @@ -87,7 +90,6 @@ Changelog
- -

Author

Michael Steinbaugh, Rory Kirchner

@@ -151,7 +150,7 @@

Author

-

Site built with pkgdown 1.3.0.9100.

+

Site built with pkgdown 1.4.0.

diff --git a/docs/reference/bcbioSingleCell-package.html b/docs/reference/bcbioSingleCell-package.html index c4d907b66..9c0a76230 100644 --- a/docs/reference/bcbioSingleCell-package.html +++ b/docs/reference/bcbioSingleCell-package.html @@ -8,11 +8,13 @@ bcbioSingleCell — bcbioSingleCell-package • bcbioSingleCell + + @@ -34,14 +36,15 @@ - + + @@ -69,7 +72,7 @@ bcbioSingleCell - 0.4.3 + 0.4.4 @@ -88,7 +91,6 @@ Changelog -

Author

Maintainer: Michael Steinbaugh mike@steinbaugh.com (0000-0002-2403-2221)

@@ -165,7 +164,7 @@

Author

-

Site built with pkgdown 1.3.0.9100.

+

Site built with pkgdown 1.4.0.

diff --git a/docs/reference/bcbioSingleCell.html b/docs/reference/bcbioSingleCell.html index 0a0257de4..9306bd651 100644 --- a/docs/reference/bcbioSingleCell.html +++ b/docs/reference/bcbioSingleCell.html @@ -8,11 +8,13 @@ bcbio single-cell RNA-seq data set — bcbioSingleCell • bcbioSingleCell + + @@ -34,8 +36,8 @@ - + @@ -71,7 +74,7 @@ bcbioSingleCell - 0.4.3 + 0.4.4 @@ -90,7 +93,6 @@ Changelog - -

Examples

uploadDir <- system.file("extdata/indrops", package = "bcbioSingleCell")
 
 x <- bcbioSingleCell(uploadDir)
#> Dated project directory: 2018-01-01_bcbio.
#> 1 sample detected:
 #> [1] "multiplexed_AAAAAAAA"
#> Importing 'project-summary.yaml' using 'yaml::yaml.load_file()'.
#> Data versions are missing.
#> Importing 'programs.txt' using 'data.table::fread()'.
#> Importing 'bcbio-nextgen.log' using 'base::readLines()'.
#> 'bcbio-nextgen.log' file is empty.
#> Importing 'bcbio-nextgen-commands.log' using 'base::readLines()'.
#> 1000 reads per cellular barcode cutoff detected.
#> Counts will imported as genes.
#> UMI type: harvard-indrop-v3.
#> Importing unfiltered cellular barcode distributions...
#> Importing 'multiplexed-AAAAAAAA-barcodes.tsv' using 'data.table::fread()'.
#> Importing counts...
#> Importing 'multiplexed-AAAAAAAA.mtx.rownames' using 'base::readLines()'.
#> Importing 'multiplexed-AAAAAAAA.mtx.colnames' using 'base::readLines()'.
#> Importing 'multiplexed-AAAAAAAA.mtx' using 'Matrix::readMM()'.
#> Importing sidecar 'multiplexed-AAAAAAAA.mtx.rownames'.
#> Importing 'multiplexed-AAAAAAAA.mtx.rownames' using 'base::readLines()'.
#> Importing sidecar 'multiplexed-AAAAAAAA.mtx.colnames'.
#> Importing 'multiplexed-AAAAAAAA.mtx.colnames' using 'base::readLines()'.
#> 'multiplexed-AAAAAAAA.mtx' does not contain syntactically valid names.
#> Imported 'multiplexed-AAAAAAAA'.
#> bcbio GTF file: /n/app/bcbio/dev/genomes/Hsapiens/hg38/rnaseq/ref-transcripts.gtf.
#> bcbio GTF file is not accessible.
#> Slotting empty ranges into 'rowRanges()'.
#> 'sampleMetadataFile' is recommended for multiplexed samples (e.g. harvard-indrop-v3).
#> Calculating 100 sample metrics.
#> Calculating metrics without biotype information.
-#> 'rowRanges' required to calculate: nCoding, nMito, mitoRatio.
print(x)
#> bcbioSingleCell 0.4.3
-#> uploadDir: /Users/mike/R/x86_64-apple-darwin15.6.0-library/3.6/bcbioSingleCell/extdata/indrops
-#> dates(2): [bcbio] 2018-01-01; [R] 2019-08-27
+#> 'rowRanges' required to calculate: nCoding, nMito, mitoRatio.
print(x)
#> bcbioSingleCell 0.4.4
+#> uploadDir: /tmp/RtmpzwtPV8/temp_libpath9c5a3896d068/bcbioSingleCell/extdata/indrops
+#> dates(2): [bcbio] 2018-01-01; [R] 2019-09-09
 #> level: genes
 #> interestingGroups: sampleName
 #> filtered: FALSE
@@ -258,11 +254,11 @@ 
Examp
     sampleMetadataFile = file.path(uploadDir, "metadata.csv")
 )
#> Dated project directory: 2018-01-01_bcbio.
#> 1 sample detected:
 #> [1] "multiplexed_AAAAAAAA"
#> Importing 'project-summary.yaml' using 'yaml::yaml.load_file()'.
#> Data versions are missing.
#> Importing 'programs.txt' using 'data.table::fread()'.
#> Importing 'bcbio-nextgen.log' using 'base::readLines()'.
#> 'bcbio-nextgen.log' file is empty.
#> Importing 'bcbio-nextgen-commands.log' using 'base::readLines()'.
#> 1000 reads per cellular barcode cutoff detected.
#> Counts will imported as genes.
#> UMI type: harvard-indrop-v3.
#> Importing 'metadata.csv' using 'data.table::fread()'.
#> Multiplexed samples detected.
#> Importing unfiltered cellular barcode distributions...
#> Importing 'multiplexed-AAAAAAAA-barcodes.tsv' using 'data.table::fread()'.
#> Importing counts...
#> Importing 'multiplexed-AAAAAAAA.mtx.rownames' using 'base::readLines()'.
#> Importing 'multiplexed-AAAAAAAA.mtx.colnames' using 'base::readLines()'.
#> Importing 'multiplexed-AAAAAAAA.mtx' using 'Matrix::readMM()'.
#> Importing sidecar 'multiplexed-AAAAAAAA.mtx.rownames'.
#> Importing 'multiplexed-AAAAAAAA.mtx.rownames' using 'base::readLines()'.
#> Importing sidecar 'multiplexed-AAAAAAAA.mtx.colnames'.
#> Importing 'multiplexed-AAAAAAAA.mtx.colnames' using 'base::readLines()'.
#> 'multiplexed-AAAAAAAA.mtx' does not contain syntactically valid names.
#> Imported 'multiplexed-AAAAAAAA'.
#> bcbio GTF file: /n/app/bcbio/dev/genomes/Hsapiens/hg38/rnaseq/ref-transcripts.gtf.
#> bcbio GTF file is not accessible.
#> Slotting empty ranges into 'rowRanges()'.
#> Calculating 100 sample metrics.
#> Calculating metrics without biotype information.
-#> 'rowRanges' required to calculate: nCoding, nMito, mitoRatio.
print(x)
#> bcbioSingleCell 0.4.3
-#> uploadDir: /Users/mike/R/x86_64-apple-darwin15.6.0-library/3.6/bcbioSingleCell/extdata/indrops
-#> dates(2): [bcbio] 2018-01-01; [R] 2019-08-27
+#> 'rowRanges' required to calculate: nCoding, nMito, mitoRatio.
print(x)
#> bcbioSingleCell 0.4.4
+#> uploadDir: /tmp/RtmpzwtPV8/temp_libpath9c5a3896d068/bcbioSingleCell/extdata/indrops
+#> dates(2): [bcbio] 2018-01-01; [R] 2019-09-09
 #> level: genes
-#> sampleMetadataFile: /Users/mike/R/x86_64-apple-darwin15.6.0-library/3.6/bcbioSingleCell/extdata/indrops/metadata.csv
+#> sampleMetadataFile: /tmp/RtmpzwtPV8/temp_libpath9c5a3896d068/bcbioSingleCell/extdata/indrops/metadata.csv
 #> interestingGroups: sampleName
 #> filtered: FALSE
 #> class: SingleCellExperiment 
@@ -282,15 +278,10 @@ 
Examp
     
Contents

     
 
@@ -306,7 +297,7 @@ 
Author

 

 
 

-  
Site built with pkgdown 1.3.0.9100.

+  
Site built with pkgdown 1.4.0.

 

 
       
diff --git a/docs/reference/bcbioSingleCellTestsURL.html b/docs/reference/bcbioSingleCellTestsURL.html
index 47e66e18f..472af7735 100644
--- a/docs/reference/bcbioSingleCellTestsURL.html
+++ b/docs/reference/bcbioSingleCellTestsURL.html
@@ -8,11 +8,13 @@
 
 Cache URL — bcbioSingleCellTestsURL • bcbioSingleCell
 
+
 
 
 
 
 
+
 
 
 
@@ -34,13 +36,14 @@
 
   
   
-
 
+
 
 
 
 
 
+
 
 
 
@@ -68,7 +71,7 @@
       
       
         bcbioSingleCell
-        0.4.3
+        0.4.4
       
     
 
@@ -87,7 +90,6 @@
   Changelog
 
       
-      
       
    
         
  • 
   
@@ -114,17 +116,15 @@ 
    Cache URL
    
     
 
     
    
-    
     
    Cache URL
    
-    
     
    
 
     
    bcbioSingleCellTestsURL
    
-        
+
+
     
    Format
    
 
     
    An object of class character of length 1.
    
-    
 
     
    Examples
    
     
    bcbioSingleCellTestsURL
    #> [1] "http://tests.acidgenomics.com/bcbioSingleCell/v0.4"
    
@@ -132,9 +132,7 @@ 
    Examp
   
 
 
    
-  
    Site built with pkgdown 1.3.0.9100.
    
+  
    Site built with pkgdown 1.4.0.
    
 
    
 
       
diff --git a/docs/reference/defunct.html b/docs/reference/defunct.html
index bdda40f5d..dda921c64 100644
--- a/docs/reference/defunct.html
+++ b/docs/reference/defunct.html
@@ -8,11 +8,13 @@
 
 Defunct functions — defunct • bcbioSingleCell
 
+
 
 
 
 
 
+
 
 
 
@@ -34,13 +36,14 @@
 
   
   
-
 
+
 
 
 
 
 
+
 
 
 
@@ -68,7 +71,7 @@
       
       
         bcbioSingleCell
-        0.4.3
+        0.4.4
       
     
 
@@ -87,7 +90,6 @@
   Changelog
 
    • 
       

-      
       
-      
       
-      
       
    
         
  • 
   
@@ -114,14 +116,12 @@ 
    Extract or replace parts of an object
    
     
 
     
    
-    
     
    Extract genes by row and cells by column.
    
-    
     
    
 
     
    # S4 method for bcbioSingleCell,ANY,ANY,ANY
 [(x, i, j, ..., drop = FALSE)
    
-    
+
     
    Arguments
    
     
@@ -138,10 +138,10 @@ 
    Arg
     Character vectors will be matched to the names of the
     object (or for matrices/arrays, the dimnames):
     see ‘Character indices’ below for further details.
    
-
    For [-indexing only: i, j, … can be
+
    For [-indexing only: i, j, ... can be
     logical vectors, indicating elements/slices to select.  Such vectors
     are recycled if necessary to match the corresponding extent.
-    i, j, … can also be negative integers,
+    i, j, ... can also be negative integers,
     indicating elements/slices to leave out of the selection.
    
 
    When indexing arrays by [ a single argument i can be a
     matrix with as many columns as there are dimensions of x; the
@@ -158,10 +158,10 @@ 
    Arg
     Character vectors will be matched to the names of the
     object (or for matrices/arrays, the dimnames):
     see ‘Character indices’ below for further details.
    
-
    For [-indexing only: i, j, … can be
+
    For [-indexing only: i, j, ... can be
     logical vectors, indicating elements/slices to select.  Such vectors
     are recycled if necessary to match the corresponding extent.
-    i, j, … can also be negative integers,
+    i, j, ... can also be negative integers,
     indicating elements/slices to leave out of the selection.
    
 
    When indexing arrays by [ a single argument i can be a
     matrix with as many columns as there are dimensions of x; the
@@ -181,11 +181,10 @@ 
    Arg
     drop for further details.
    
     
     
    
     
    
-    
+
     
    Value
    
 
     
    bcbioSingleCell.
    
-    
     
    Details
    
 
     
    Refer to cell2sample() and
@@ -195,17 +194,14 @@ 
    Details
 
    Unfiltered cellular barcode distributions for the entire dataset, including
 cells not kept in the matrix will be dropped in favor of the nCount column
 of colData().
    
-    
     
    Note
    
 
     
    Updated 2019-08-20.
    
-    
     
    References
    
 
     
    Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988)
   The New S Language.
   Wadsworth & Brooks/Cole.
    
-    
 
     
    Examples
    
     
    data(bcb)
@@ -283,15 +279,10 @@ 
    Examp
     
    Contents
    
     
 
@@ -307,7 +298,7 @@ 
    Author
    
 
    
 
 
    
-  
    Site built with pkgdown 1.3.0.9100.
    
+  
    Site built with pkgdown 1.4.0.
    
 
    
 
       
diff --git a/docs/reference/index.html b/docs/reference/index.html
index c264f85f1..9a1eade68 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -8,11 +8,13 @@
 
 Function reference • bcbioSingleCell
 
+
 
 
 
 
 
+
 
 
 
@@ -34,10 +36,12 @@
 
   
   
+
 
 
 
 
+
 
 
 
@@ -65,7 +69,7 @@
       
       
         bcbioSingleCell
-        0.4.3
+        0.4.4
       
     
 
@@ -84,7 +88,6 @@
   Changelog
 
    • 
       

-      
       
-      
       
-      
       
 
   
 
@@ -149,7 +152,7 @@ 
Contents

 
 
 

-  
Site built with pkgdown 1.3.0.9100.

+  
Site built with pkgdown 1.4.0.

 

 
       
diff --git a/docs/reference/show.html b/docs/reference/show.html
index 4b68bd58b..9f4b17865 100644
--- a/docs/reference/show.html
+++ b/docs/reference/show.html
@@ -8,11 +8,13 @@
 
 Show an object — show • bcbioSingleCell
 
+
 
 
 
 
 
+
 
 
 
@@ -34,8 +36,8 @@
 
   
   
-
 
+
 
 
@@ -72,7 +75,7 @@
       
       
         bcbioSingleCell
-        0.4.3
+        0.4.4
       
     
 
@@ -91,7 +94,6 @@
   Changelog
 
       
-      
       
-      
       
    
         
  • 
   
@@ -115,15 +117,13 @@ 
    Update an object to its current class definition
    
     
 
     
    
-    
     
    updateObject is a generic function that returns an instance
   of object updated to its current class definition.
    
-    
     
    
 
     
    # S4 method for bcbioSingleCell
 updateObject(object)
    
-    
+
     
    Arguments
    
     
@@ -135,7 +135,7 @@ 
    Arg
     getObjectSlots.
    
     
     
    
     
    
-    
+
     
    Value
    
 
     
    updateObject returns a valid instance of object.
    
@@ -143,7 +143,6 @@ 
    Value
    
   objclass.
    
 
    getObjectSlots returns a list of named elements, with each
   element corresponding to a slot in object.
    
-    
     
    Details
    
 
     
    Updating objects is primarily useful when an object has been
@@ -154,7 +153,7 @@ 
    Details
   the same as the class of the argument object, and that the
   object is valid (see validObject). By default,
   updateObject has the following behaviors:
    
-    
    updateObject(ANY, …, verbose=FALSE)
    By default, updateObject uses heuristic methods to determine
+    
    updateObject(ANY, ..., verbose=FALSE)
    By default, updateObject uses heuristic methods to determine
       whether the object should be the `new' S4 type (introduced in R 2.4.0),
       but is not. If the heuristics indicate an update is required,
       the updateObjectFromSlots function tries to update the
@@ -163,35 +162,34 @@ 
    Details
       required but not possible.
       The optional named argument verbose causes a message to be
       printed describing the action.
-      Arguments … are passed to updateObjectFromSlots.
    
-    
    updateObject(list, …, verbose=FALSE)
    Visit each element in list, applying
-      updateObject(list[[elt]], …, verbose=verbose).
    
-    
    updateObject(environment, …, verbose=FALSE)
    Visit each element in environment, applying
-      updateObject(environment[[elt]], …, verbose=verbose)
    
-    
    updateObject(formula, …, verbose=FALSE)
    Do nothing; the environment of the formula may be too general
+      Arguments ... are passed to updateObjectFromSlots.
    
+    
    updateObject(list, ..., verbose=FALSE)
    Visit each element in list, applying
+      updateObject(list[[elt]], ..., verbose=verbose).
    
+    
    updateObject(environment, ..., verbose=FALSE)
    Visit each element in environment, applying
+      updateObject(environment[[elt]], ..., verbose=verbose)
    
+    
    updateObject(formula, ..., verbose=FALSE)
    Do nothing; the environment of the formula may be too general
       (e.g., R_GlobalEnv) to attempt an update.
    
-    
    updateObject(envRefClass, …, verbose=FALSE)
    Attempt to update objects from fields using a strategy like
+    
    updateObject(envRefClass, ..., verbose=FALSE)
    Attempt to update objects from fields using a strategy like
       updateObjectFromSlots Method 1.
    
-  
    
+  
+
 
-
    updateObjectFromSlots(object, objclass=class(object), …,
+
    updateObjectFromSlots(object, objclass=class(object), ...,
   verbose=FALSE) is a utility function that identifies the intersection
   of slots defined in the object instance and objclass
   definition. Under Method 1, the corresponding elements in
-  object are then updated (with updateObject(elt, …,
+  object are then updated (with updateObject(elt, ...,
   verbose=verbose)) and used as arguments to a call to new(class,
-  …), with … replaced by slots from the original
+  ...), with ... replaced by slots from the original
   object. If this fails, then Method 2 tries new(class) and
   assigns slots of object to the newly created instance.
    
 
    getObjectSlots(object) extracts the slot names and contents from
   object. This is useful when object was created by a class
   definition that is no longer current, and hence the contents of
   object cannot be determined by accessing known slots.
    
-    
     
    Note
    
 
     
    Updated 2019-08-12.
    
-    
     
    See also
    
 
     
    
@@ -209,11 +207,10 @@ 
    See a
           in the BiocGenerics package.
    • 
 

 
-    
 
     
Examples

     
data(bcb)
-updateObject(bcb)
#> Upgrading bcbioSingleCell from version 0.3.19 to 0.4.3.
#> bcbioSingleCell 0.4.3
+updateObject(bcb)
#> Upgrading bcbioSingleCell from version 0.3.19 to 0.4.4.
#> bcbioSingleCell 0.4.4
 #> uploadDir: /data00/draco/acidbase/packages/bcbioSingleCell/inst/extdata/indrops
 #> dates(2): [bcbio] 2018-01-01; [R] 2019-08-12
 #> level: genes
@@ -248,15 +245,10 @@ 
Examp
     
Contents

     
 
@@ -272,7 +264,7 @@ 
Author

 

 
 

-  
Site built with pkgdown 1.3.0.9100.

+  
Site built with pkgdown 1.4.0.

 

 
       

From 13b1b1eb9baad39ee3875f6850cdd442f9c97b00 Mon Sep 17 00:00:00 2001
From: Michael Steinbaugh 
Date: Mon, 9 Sep 2019 12:40:50 -0400
Subject: [PATCH 5/5] Update NEWS

---
 NEWS.md                 |  9 ++++++
 docs/news/news-0.1.html | 44 ++++++++++++-------------
 docs/news/news-0.2.html |  8 ++---
 docs/news/news-0.3.html | 72 ++++++++++++++++++++---------------------
 docs/news/news-0.4.html | 28 ++++++++++++----
 5 files changed, 92 insertions(+), 69 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 00293254d..a438776a6 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,12 @@
+## bcbioSingleCell 0.4.4 (2019-09-09)
+
+### Minor changes
+
+- `bcbioSingleCell`: Internal generator now calls `importSampleData` using
+  `pipeline = "bcbio"` argument, so we don't run into breaking changes when
+  handling user metadata in a future basejump update.
+- Updated basejump dependency versions.
+
 ## bcbioSingleCell 0.4.3 (2019-08-27)
 
 ### Minor changes
diff --git a/docs/news/news-0.1.html b/docs/news/news-0.1.html
index 87dd35527..a07340f37 100644
--- a/docs/news/news-0.1.html
+++ b/docs/news/news-0.1.html
@@ -132,9 +132,9 @@ 

 filterCells now supports minUMIs = c("knee", "inflection") for automatic filtering based on the cellular barcode ranks. Internally this is handled by DropletUtils::barcodeRanks.
 
 
-

+

 

-Minor changes

+Minor changes

 
    
 
  • Attempting to re-enable libgsl-dev installation for zinbwave on Travis CI.
    • 
 
  • Suggesting BiocParallel for zinbwave call in diffExp.
    • 
@@ -149,9 +149,9 @@ 
    
     
    
 
    
 bcbioSingleCell 0.1.8 (2018-05-16)
    
-
    
+
    
 
    
-Minor changes
    
+Minor changes
    
 
      
 
    • Initial updateObject method support for bcbioSingleCell class.
      • 
 
    • Relaxed validObject validity check to not require sample-level metadata in colData yet.
      • 
@@ -168,9 +168,9 @@ 
      
 
    • No longer attempting to sanitize the rownames for seurat objects in coercion method. This helps maintain the gene symbol appearance in plotting functions for genes with hyphens in the names.
      • 
 
    
 
-
    
+
    
 
    
-Minor changes
    
+Minor changes
 
      
 
    • Using BiocParallel::SerialParam internally for zinbwave in diffExp.
      • 
 
    • Simplified cell2sample internal code to always use mapCellsToSamples instead of attempting to use a stashed vector inside metadata for SingleCellExperiment method.
      • 
@@ -189,9 +189,9 @@ 
      
     
      
 
      
 bcbioSingleCell 0.1.10 (2018-05-19)
      
-
      
+
      
 
      
-Minor changes
      
+Minor changes
      
 
        
 
      • 
 plotCellTypesPerCluster is using dark = TRUE by default again.
        • 
@@ -224,9 +224,9 @@ 
        
 aggregateReplicates function has been reworked to return a SingleCellExperiment object instead of bcbioSingleCell. The v0.2.4 update of bcbioRNASeq behaves similarly with this generic.
 
      
 
    
-
    
+
    
 
    
-Minor changes
    
+Minor changes
 
      
 
    • Reworked the internal handling of some seurat SingleCellExperiment method support, using as(x, "SingleCellExperiment") internally, which uses the new Seurat::Convert function.
      • 
 
    • Made some previously deprecated functions now defunct: plotClusters, plotTSNEExpressionData, loadSingleCellRun, darkTheme, pcCutoff, quantileHeatmap, plotKnownMarkers, readMarkers, readMarkersFile.
      • 
@@ -249,9 +249,9 @@ 
      
 
    • Improved R Markdown clustering and marker templates to optionally support UMAP and dark mode in the YAML parameters.
      • 
 
    
 
    
-
    
+
    
 
    
-Minor changes
    
+Minor changes
 
      
 
    • Using original Seurat mapping names for data: tSNE_1, tSNE_2, PC1, PC2, UMAP1, UMAP2.
      • 
 
    • Ensure transcript-level counts always have stripTranscriptVersions command applied, to remove the Ensembl transcript versions if present.
      • 
@@ -263,9 +263,9 @@ 
      
     
      
 
      
 bcbioSingleCell 0.1.13 (2018-05-29)
      
-
      
+
      
 
      
-Minor changes
      
+Minor changes
      
 
        
 
      • t-SNE and UMAP plot improvements.
        • 
 
      
@@ -283,9 +283,9 @@ 
      
 readCellRanger no longer requires reference data defined by refdataDir, although this is still recommended.
 
    
 
    
-
    
+
    
 
    
-Minor changes
    
+Minor changes
 
      
 
    • Resaved example datasets.
      • 
 
    • Switched the example cellranger_small and seurat_small datasets to the publicly available pbmc4k dataset from 10X Genomics. Here we’ve subset the top 500 cells and genes by abundance. We’ll use either the pbmc4k or pbmc8k dataset for the vignette in a future update.
      • 
@@ -307,9 +307,9 @@ 
      
     
      
 
      
 bcbioSingleCell 0.1.15 (2018-06-13)
      
-
      
+
      
 
      
-Minor changes
      
+Minor changes
      
 
        
 
      • Updated internal code to use text as primary argument in markdownHeader calls.
        • 
 
      • Updated example datasets and unit tests to match.
        • 
@@ -337,9 +337,9 @@ 
        
 Seurat clustering now calculates multiple resolutions, suggesting 0.4, 0.8, and 1.2 by default. Dimensional reduction plots have been updated to support looping of these multiple resolutions.
 
      
 
    
-
    
+
    
 
    
-Minor changes
    
+Minor changes
 
      
 
    • 
 as(object, "SingleCellExperiment") coercion now slots stashed metadata into SingleCellExperiment, if defined.
      • 
@@ -368,9 +368,9 @@ 
      
 
    • Internal data has been renamed to snake_case format, for improved consistency. Note that cell_cycle_markers is used in place of cellCycleMarkers, and cell_type_markers in place of cellTypeMarkers. There’s no easy way to link these files as aliases, so this is a necessary breaking change.
      • 
 
    
 
    
-
    
+
    
 
    
-Minor changes
    
+Minor changes
 
      
 
    • Improved R Markdown template defaults for quality control and clustering.
      • 
 
    • Now importing functions related to differential expression into the package NAMESPACE, including DESeq2, edgeR, and zinbwave.
      • 
diff --git a/docs/news/news-0.2.html b/docs/news/news-0.2.html
index 950b459d5..9b18e822d 100644
--- a/docs/news/news-0.2.html
+++ b/docs/news/news-0.2.html
@@ -131,9 +131,9 @@ 
      
 
    • Removed from exports (for simplicifcation): plotClusters, plotFeatures, quantileHeatmap, readMarkers, readMarkersFile.
      • 
 
    
 
    
-
    
+
    
 
    
-Minor changes
    
+Minor changes
 
      
 
    • No longer exporting mapCellsToSamples. This is now only called internally.
      • 
 
    • Updated documentation to use roxygen2 v6.1.
      • 
@@ -150,9 +150,9 @@ 
      
 
    • Moved clustering and marker templates to pointillism package, since all clustering code has been moved there. The quality control template using the filterCells function is still provided here.
      • 
 
    
 
    
-
    
+
    
 
    
-Minor changes
    
+Minor changes
 
      
 
    • 
 prepareSingleCellTemplate: Improved internal code to use updated prepareTemplate, which has been migrated to basejump package.
      • 
diff --git a/docs/news/news-0.3.html b/docs/news/news-0.3.html
index 247dc430f..c48cacf2a 100644
--- a/docs/news/news-0.3.html
+++ b/docs/news/news-0.3.html
@@ -132,9 +132,9 @@ 
      
 
    • Reorganized metricsPerSample code approach.
      • 
 
    
 
    
-
    
+
    
 
    
-Minor changes
    
+Minor changes
 
      
 
    • Consolidated S4 validity check code into AllClasses.R file.
      • 
 
    • Updated Travis and AppVeyor CI configuration.
      • 
@@ -158,9 +158,9 @@ 
      
 
    • Renamed example data from cellranger_small to cellranger, and indrops_small to simply indrops.
      • 
 
    
 
    
-
    
+
    
 
    
-Minor changes
    
+Minor changes
 
      
 
    • Transitioning to goalie for assert checks in place of assertive package.
      • 
 
    • Miscellaneous documentation improvements.
      • 
@@ -185,9 +185,9 @@ 
      
 
    • Improved plotting functions to inherit params from basejump.
      • 
 
    
 
    
-
    
+
    
 
    
-Minor changes
    
+Minor changes
 
      
 
    • Removed barcodePattern global variable.
      • 
 
    
@@ -196,9 +196,9 @@ 
    
     
    
 
    
 bcbioSingleCell 0.3.3 (2018-11-25)
    
-
    
+
    
 
    
-Minor changes
    
+Minor changes
    
 
      
 
    • Updated basejump and bcbioBase dependencies, to tighten up build checks.
      • 
 
    • Documentation and CI configuration fixes.
      • 
@@ -216,9 +216,9 @@ 
      
 metrics: Removed code and consolidated SingleCellExperiment method support in basejump package.
 
    
 
    
-
    
+
    
 
    
-Minor changes
    
+Minor changes
 
      
 
    • Documentation improvements.
      • 
 
    • 
@@ -240,9 +240,9 @@ 
      
 
    • Migrated to inheriting S4 generics from bioverbs, where applicable.
      • 
 
    
 
    
-
    
+
    
 
    
-Minor changes
    
+Minor changes
 
      
 
    • Reworked documentation to use sentence case instead of title case.
      • 
 
    
@@ -251,9 +251,9 @@ 
    
     
    
 
    
 bcbioSingleCell 0.3.6 (2019-01-13)
    
-
    
+
    
 
    
-Minor changes
    
+Minor changes
    
 
      
 
    • Updated basejump and bcbioBase dependencies, to pass build checks.
      • 
 
    • Split out imports into a separate R file.
      • 
@@ -263,9 +263,9 @@ 
      
     
      
 
      
 bcbioSingleCell 0.3.7 (2019-02-12)
      
-
      
+
      
 
      
-Minor changes
      
+Minor changes
      
 
        
 
      • 
 bcbioSingleCell generator: improved internal handling of mapCellsToSamples call. This reworked join step checks the sampleID mapping more carefully.
        • 
@@ -276,9 +276,9 @@ 
        
     
        
 
        
 bcbioSingleCell 0.3.8 (2019-03-18)
        
-
        
+
        
 
        
-Minor changes
        
+Minor changes
        
 
          
 
        • Updated basejump and bcbioBase dependencies.
          • 
 
        • Updated documentation.
          • 
@@ -289,9 +289,9 @@ 
          
     
          
 
          
 bcbioSingleCell 0.3.9 (2019-04-01)
          
-
          
+
          
 
          
-Minor changes
          
+Minor changes
          
 
            
 
          • Migrated development code to Acid Genomics.
            • 
 
          • Updated basejump dependency to v0.10 release series.
            • 
@@ -311,9 +311,9 @@ 
            
 
          • Extract method [ on bcbioSingleCell class objects no longer alters the version of the object. It only sets subset = TRUE, similar to bcbioRNASeq.
            • 
 
          
 
    
-
    
+
    
 
    
-Minor changes
    
+Minor changes
 
      
 
    • Bug fix release for formal rename in emptyRanges from mcolsNames to mcolnames. This has been changed in basejump 0.10.3.
      • 
 
    
@@ -329,9 +329,9 @@ 
    
 
  • Restricted S4 methods back to bcbioSingleCell from SingleCellExperiment where applicable. Generally, this applies to the supported QC plotting functions. Previously, the methods were defined against SingleCellExperiment to also support CellRanger S4 class, which has since been moved to the Chromium package.
    • 
 

 
-

+

 

-Minor changes

+Minor changes
 
    
 
  • Improved code coverage by adding additional unit tests.
    • 
 
  • Updated internal reexport method for S4 generics, making reexports.Rd file no longer necessary.
    • 
@@ -342,9 +342,9 @@ 
    
     
    
 
    
 bcbioSingleCell 0.3.12 (2019-04-18)
    
-
    
+
    
 
    
-Minor changes
    
+Minor changes
    
 
      
 
    • Deprecated prepareSingleCellTemplate, in favor of prepareTemplate.
      • 
 
    • Switched Travis CI configuration to use singlecell Docker image.
      • 
@@ -354,9 +354,9 @@ 
      
     
      
 
      
 bcbioSingleCell 0.3.13 (2019-04-23)
      
-
      
+
      
 
      
-Minor changes
      
+Minor changes
      
 
        
 
      • Now importing ggplot2 code from acidplots package.
        • 
 
      • 
@@ -375,9 +375,9 @@ 
        
     
        
 
        
 bcbioSingleCell 0.3.15 (2019-05-29)
        
-
        
+
        
 
        
-Minor changes
        
+Minor changes
        
 
          
 
        • Updated barcodeRanksPerSample and plotBarcodeRanks to support DropletUtils update in Bioconductor 3.9.
          • 
 
        • Improved Travis and AppVeyor CI configuration.
          • 
@@ -387,9 +387,9 @@ 
          
     
          
 
          
 bcbioSingleCell 0.3.16 (2019-07-17)
          
-
          
+
          
 
          
-Minor changes
          
+Minor changes
          
 
            
 
          • Updated basejump dependencies.
            • 
 
          • Improved Travis CI docker configuration.
            • 
@@ -399,9 +399,9 @@ 
            
     
            
 
            
 bcbioSingleCell 0.3.17 (2019-07-24)
            
-
            
+
            
 
            
-Minor changes
            
+Minor changes
            
 
              
 
            • Improved internal S4 function naming consistency.
              • 
 
            • Updated basejump dependencies.
              • 
@@ -420,9 +420,9 @@ 
              
 updateObject: Simplified method support, dropping rowRanges argument. No longer attempting to coerce assays back to a simple list, which doesn’t work well on Bioconductor 3.10 Devel currently.
 
            
 

-

+

 

-Minor changes

+Minor changes
 
    
 
  • Updated basejump dependencies.
    • 
 
  • Improved code coverage over 90%.
    • 
diff --git a/docs/news/news-0.4.html b/docs/news/news-0.4.html
index 70e6d3074..c1e2bd459 100644
--- a/docs/news/news-0.4.html
+++ b/docs/news/news-0.4.html
@@ -123,9 +123,9 @@ 
    
 
  • Offloaded plotting functions to acidplots, so we can use some of this code in a shared manner with objects imported from 10X Genomics Chromium.
    • 
 

 

-

+

 

-Minor changes

+Minor changes
 
    
 
  • Improved documentation consistency by using shared roxygen from acidroxygen package.
    • 
 
  • Updated basejump and bcbio R package dependencies.
    • 
@@ -135,9 +135,9 @@ 
    
     
    
 
    
 bcbioSingleCell 0.4.1 (2019-08-20)
    
-
    
+
    
 
    
-Minor changes
    
+Minor changes
    
 
      
 
    • 
 plotReadsPerCell: Reworked internal code to use DataFrame primarily instead of tbl_df, so we can remove dplyr dependency.
      • 
@@ -157,9 +157,9 @@ 
      
 bcbioSingleCell: Simplifed internal colData handling, calling calculateMetrics after creating SingleCellExperiment with makeSingleCellExperiment. This improves consistency with Chromium package and enables better preparation of rowRanges containing spike-ins and transgenes.
 
    
 

-

+

 

-Minor changes

+Minor changes
 
    
 
  • Moved metricsCols global to basejump, so we can share with Chromium.
    • 
 
  • Improved generator consistency with other basejump and bcbio R packages.
    • 
@@ -169,11 +169,24 @@ 
    
     
    
 
    
 bcbioSingleCell 0.4.3 (2019-08-27)
    
+
    
+
    
+Minor changes
    
+
      
+
    • NAMESPACE and basejump dependency updates.
      • 
+
    
+
    
+
    
+    
    
+
    
+bcbioSingleCell 0.4.4 (2019-09-09)
    
 
    
 
    
 Minor changes
    
 
      
-
    • NAMESPACE and basejump dependency updates.
      • 
+
    • 
+bcbioSingleCell: Internal generator now calls importSampleData using pipeline = "bcbio" argument, so we don’t run into breaking changes when handling user metadata in a future basejump update.
      • 
+
    • Updated basejump dependency versions.
      • 
 
    
 
    
 
    
@@ -187,6 +200,7 @@ 
    Contents
    
         
  • 0.4.1
    • 
         
  • 0.4.2
    • 
         
  • 0.4.3
    • 
+        
  • 0.4.4
    •