diff --git a/404.html b/404.html index eae6591..6d0a8ad 100644 --- a/404.html +++ b/404.html @@ -6,7 +6,7 @@ Page not found (404) • CytoPipeline - + @@ -32,7 +32,7 @@ CytoPipeline - 1.3.6 + 1.5.1 @@ -103,7 +103,7 @@

Page not found (404)

-

Site built with pkgdown 2.0.7.9000.

+

Site built with pkgdown 2.0.9.9000.

diff --git a/LICENSE-text.html b/LICENSE-text.html index 0499953..f2f855e 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -1,5 +1,5 @@ -License • CytoPipelineLicense • CytoPipeline @@ -17,7 +17,7 @@ CytoPipeline - 1.3.6 + 1.5.1 @@ -105,7 +105,7 @@

License

-

Site built with pkgdown 2.0.7.9000.

+

Site built with pkgdown 2.0.9.9000.

diff --git a/articles/CytoPipeline.html b/articles/CytoPipeline.html index 4097bbd..ffd24ae 100644 --- a/articles/CytoPipeline.html +++ b/articles/CytoPipeline.html @@ -6,7 +6,7 @@ Automation and Visualization of Flow Cytometry Data Analysis Pipelines • CytoPipeline - + @@ -33,7 +33,7 @@ CytoPipeline - 1.3.6 + 1.5.1 @@ -493,8 +493,6 @@

Executing PeacoQC pipeline## margin event in file Donor1.fcs . This should be verified. 
## Removing margins from file : Donor2.fcs
## Proceeding with step 3 [compensate] ...
-
## Compensating file : Donor1.fcs
-
## Compensating file : Donor2.fcs
## Proceeding with step 4 [flowframe_aggregate] ...
## Proceeding with step 5 [scale_transform_estimate] ...
## #####################################################
@@ -507,7 +505,6 @@

Executing PeacoQC pipeline## channel_specifications = PQCChannelSpecs): More than 10.12 % is considered as a ## margin event in file Donor1.fcs . This should be verified. 
## Proceeding with step 3 [compensate] ...
-
## Compensating file : Donor1.fcs
## Proceeding with step 4 [perform_QC] ...
## Applying PeacoQC method...
## Starting quality control analysis for Donor1.fcs
@@ -529,7 +526,6 @@

Executing PeacoQC pipeline## Proceeding with step 2 [remove_margins] ... 
## Removing margins from file : Donor2.fcs
## Proceeding with step 3 [compensate] ...
-
## Compensating file : Donor2.fcs
## Proceeding with step 4 [perform_QC] ...
## Applying PeacoQC method...
## Starting quality control analysis for Donor2.fcs
@@ -551,7 +547,7 @@

Executing flowAI pipelineNote: again this might generate some warnings, due to flowAI.
These are highly dependent on the shape of the data investigated, and can safely be ignored here.

-
+
 # execute flowAI pipeline
 execute(pipL_flowAI, path = workDir)

 
## #####################################################

@@ -565,8 +561,6 @@ 
Executing flowAI pipeline## margin event in file Donor1.fcs . This should be verified.
## Removing margins from file : Donor2.fcs
## Proceeding with step 3 [compensate] ...
-
## Compensating file : Donor1.fcs
-
## Compensating file : Donor2.fcs
## Proceeding with step 4 [flowframe_aggregate] ...
## Proceeding with step 5 [scale_transform_estimate] ...
## #####################################################
@@ -580,7 +574,6 @@

Executing flowAI pipeline## 0% of anomalous cells detected in signal acquisition check. ## 0.12% of anomalous cells detected in the dynamic range check. 
## Proceeding with step 3 [compensate] ...
-
## Compensating file : Donor1.fcs
## Proceeding with step 4 [remove_doublets] ...
## Proceeding with step 5 [remove_debris] ...
## Proceeding with step 6 [remove_dead_cells] ...
@@ -595,7 +588,6 @@

Executing flowAI pipeline## 0% of anomalous cells detected in signal acquisition check. ## 0.1% of anomalous cells detected in the dynamic range check. 
## Proceeding with step 3 [compensate] ...
-
## Compensating file : Donor2.fcs
## Proceeding with step 4 [remove_doublets] ...
## Proceeding with step 5 [remove_debris] ...
## Proceeding with step 6 [remove_dead_cells] ...
@@ -607,7 +599,7 @@

Inspecting results and visualizati

Plotting processing queues as workflow graphs

-
+
 # plot work flow graph - PeacoQC - scale transformList
 plotCytoPipelineProcessingQueue(
   pipL_PeacoQC,
@@ -618,7 +610,7 @@ 
Plotting processing queue
 PeacoQC pipeline - scale transformList processing queue
 

 

-
+
 # plot work flow graph - PeacoQC - pre-processing
 plotCytoPipelineProcessingQueue(
   pipL_PeacoQC,
@@ -630,7 +622,7 @@ 
Plotting processing queue
 PeacoQC pipeline - file pre-processing queue
 

 

-
+
 # plot work flow graph - flowAI - scale transformList
 plotCytoPipelineProcessingQueue(
   pipL_flowAI,
@@ -641,7 +633,7 @@ 
Plotting processing queue
 flowAI pipeline - scale transformList processing queue
 

 

-
+
 # plot work flow graph - flowAI - pre-processing
 
 plotCytoPipelineProcessingQueue(
@@ -658,7 +650,7 @@ 
Plotting processing queue
 

 
Obtaining information about pipeline generated objects
 

-
+
 getCytoPipelineObjectInfos(pipL_PeacoQC, 
                            path = workDir,
                            whichQueue = "scale transform")

@@ -668,7 +660,7 @@ 
Obtaining inform
 ## 3               compensate_obj       flowSet
 ## 4      flowframe_aggregate_obj     flowFrame
 ## 5 scale_transform_estimate_obj transformList

-
+
 getCytoPipelineObjectInfos(pipL_PeacoQC, 
                            path = workDir,
                            whichQueue = "pre-processing",
@@ -685,7 +677,7 @@ 
Obtaining inform
 

 
Retrieving flow frames at different steps and plotting them
 

-
+
 # example of retrieving a flow frame
 # at a given step
 ff <- getCytoPipelineFlowFrame(
@@ -702,14 +694,14 @@ 
Retrieving
   sampleFile = 1,
   objectName = "remove_debris_obj",
   path = workDir)

-
+
 ggplotEvents(ff, xChannel = "FSC-A")

 

 1-dimensional distribution plot (forward scatter channel)

 1-dimensional distribution plot (forward scatter channel)
 

 

-
+
 ggplotEvents(ff, xChannel = "FSC-A", yChannel = "SSC-A")

 

 2-dimensional distribution plot (forward scatter vs. side scatter channels)

@@ -717,7 +709,7 @@ 
Retrieving
 channels)
 

 

-
+
 ggplotFilterEvents(ff, ff2, xChannel = "FSC-A", yChannel = "SSC-A")

 

 2-dimensional difference plot between remove_doublets and remove_debris steps

@@ -735,7 +727,7 @@ 
Example of retrieving anot
 represents a set of
flowCore::flowFrameobjects, that was obtained after the
 compensation step of the scale transformation processing queue, prior to
 aggregating the two samples.

-
+
 obj <- getCytoPipelineObjectFromCache(pipL_PeacoQC,
                                       path = workDir,
                                       whichQueue = "scale transform",
@@ -754,7 +746,7 @@ 
Getting an
 
This can be implemented using CytoPipeline
 collectNbOfRetainedEvents() function. Examples of using
 this function in quality control plots are shown in this section.

-
+
 ret <- CytoPipeline::collectNbOfRetainedEvents(
     experimentName = "OMIP021_PeacoQC",
     path = workDir
@@ -766,7 +758,7 @@ 
Getting an
 ##            remove_debris remove_dead_cells
 ## Donor1.fcs          1850              1784
 ## Donor2.fcs          3019              2984

-
+
 retainedProp <- 
     as.data.frame(t(apply(
         ret,
@@ -789,7 +781,7 @@ 
Getting an
 ##            remove_dead_cells
 ## Donor1.fcs             0.357
 ## Donor2.fcs             0.597

-
+
 stepRemovedProp <- 
     as.data.frame(t(apply(
         ret,
@@ -812,10 +804,10 @@ 
Getting an
 ##            remove_dead_cells
 ## Donor1.fcs             0.036
 ## Donor2.fcs             0.012

-
+
-
+
 myGGPlot <- function(DF, title){
     stepNames = colnames(DF)
     rowNames = rownames(DF)
@@ -842,7 +834,7 @@ 
Getting an
                title = "Retained event proportion at each step")
 p1

 

-
+
 p2 <- myGGPlot(DF = stepRemovedProp,
                title = "Event proportion removed by each step")
 p2

@@ -857,7 +849,7 @@ 
Interactive visualizationflowCore::transformList. To do this, install the
 CytoPipelineGUI package, and uncomment the following
 code:

-
+
 #devtools::install_github("https://github.com/UCLouvain-CBIO/CytoPipelineGUI")
 #CytoPipelineGUI::CytoPipelineCheckApp(dir = workDir)

 

@@ -886,9 +878,9 @@ 
Adding
 

 
Session information
 

-
## R Under development (unstable) (2024-02-19 r85946)
+
## R version 4.4.0 (2024-04-24)
 ## Platform: x86_64-pc-linux-gnu
-## Running under: Ubuntu 22.04.3 LTS
+## Running under: Ubuntu 22.04.4 LTS
 ## 
 ## Matrix products: default
 ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
@@ -909,49 +901,49 @@ 
Session information## [1] stats     graphics  grDevices utils     datasets  methods   base     
 ## 
 ## other attached packages:
-## [1] ggplot2_3.5.0      reshape2_1.4.4     CytoPipeline_1.3.6 BiocStyle_2.31.0  
+## [1] ggplot2_3.5.1      reshape2_1.4.4     CytoPipeline_1.5.1 BiocStyle_2.33.0  
 ## 
 ## loaded via a namespace (and not attached):
 ##   [1] DBI_1.2.2             gridExtra_2.3         rlang_1.1.3          
 ##   [4] magrittr_2.0.3        clue_0.3-65           GetoptLong_1.0.5     
-##   [7] matrixStats_1.2.0     compiler_4.4.0        RSQLite_2.3.5        
-##  [10] png_0.1-8             systemfonts_1.0.5     vctrs_0.6.5          
+##   [7] matrixStats_1.3.0     compiler_4.4.0        RSQLite_2.3.6        
+##  [10] png_0.1-8             systemfonts_1.0.6     vctrs_0.6.5          
 ##  [13] stringr_1.5.1         pkgconfig_2.0.3       shape_1.4.6.1        
-##  [16] crayon_1.5.2          fastmap_1.1.1         dbplyr_2.4.0         
-##  [19] labeling_0.4.3        utf8_1.2.4            ncdfFlow_2.49.0      
-##  [22] rmarkdown_2.25        graph_1.81.0          ragg_1.2.7           
-##  [25] purrr_1.0.2           bit_4.0.5             xfun_0.42            
-##  [28] zlibbioc_1.49.0       cachem_1.0.8          jsonlite_1.8.8       
-##  [31] flowWorkspace_4.15.4  blob_1.2.4            highr_0.10           
+##  [16] crayon_1.5.2          fastmap_1.1.1         dbplyr_2.5.0         
+##  [19] labeling_0.4.3        utf8_1.2.4            ncdfFlow_2.51.0      
+##  [22] rmarkdown_2.26.2      graph_1.83.0          ragg_1.3.1           
+##  [25] purrr_1.0.2           bit_4.0.5             xfun_0.43            
+##  [28] zlibbioc_1.51.0       cachem_1.0.8          jsonlite_1.8.8       
+##  [31] flowWorkspace_4.17.0  blob_1.2.4            highr_0.10           
 ##  [34] parallel_4.4.0        cluster_2.1.6         R6_2.5.1             
-##  [37] bslib_0.6.1           stringi_1.8.3         RColorBrewer_1.1-3   
-##  [40] jquerylib_0.1.4       Rcpp_1.0.12           bookdown_0.37        
-##  [43] iterators_1.0.14      knitr_1.45            zoo_1.8-12           
-##  [46] IRanges_2.37.1        flowCore_2.15.2       tidyselect_1.2.0     
-##  [49] yaml_2.3.8            doParallel_1.0.17     codetools_0.2-19     
-##  [52] curl_5.2.0            lattice_0.22-5        tibble_3.2.1         
-##  [55] plyr_1.8.9            Biobase_2.63.0        withr_3.0.0          
-##  [58] evaluate_0.23         desc_1.4.3            BiocFileCache_2.11.1 
-##  [61] circlize_0.4.16       pillar_1.9.0          BiocManager_1.30.22  
-##  [64] filelock_1.0.3        foreach_1.5.2         flowAI_1.33.0        
+##  [37] bslib_0.7.0           stringi_1.8.4         RColorBrewer_1.1-3   
+##  [40] jquerylib_0.1.4       Rcpp_1.0.12           bookdown_0.39        
+##  [43] iterators_1.0.14      knitr_1.46            zoo_1.8-12           
+##  [46] IRanges_2.39.0        flowCore_2.17.0       tidyselect_1.2.1     
+##  [49] yaml_2.3.8            doParallel_1.0.17     codetools_0.2-20     
+##  [52] curl_5.2.1            lattice_0.22-6        tibble_3.2.1         
+##  [55] plyr_1.8.9            Biobase_2.65.0        withr_3.0.0          
+##  [58] evaluate_0.23         desc_1.4.3            BiocFileCache_2.13.0 
+##  [61] circlize_0.4.16       pillar_1.9.0          BiocManager_1.30.23  
+##  [64] filelock_1.0.3        foreach_1.5.2         flowAI_1.35.0        
 ##  [67] stats4_4.4.0          generics_0.1.3        diagram_1.6.5        
-##  [70] S4Vectors_0.41.3      munsell_0.5.0         ggcyto_1.31.1        
-##  [73] scales_1.3.0          PeacoQC_1.13.0        glue_1.7.0           
+##  [70] S4Vectors_0.43.0      munsell_0.5.1         ggcyto_1.33.0        
+##  [73] scales_1.3.0          PeacoQC_1.15.0        glue_1.7.0           
 ##  [76] changepoint_2.2.4     tools_4.4.0           hexbin_1.28.3        
-##  [79] data.table_1.15.0     fs_1.6.3              XML_3.99-0.16.1      
-##  [82] grid_4.4.0            RProtoBufLib_2.15.0   colorspace_2.1-0     
+##  [79] data.table_1.15.4     fs_1.6.4              XML_3.99-0.16.1      
+##  [82] grid_4.4.0            RProtoBufLib_2.17.0   colorspace_2.1-0     
 ##  [85] cli_3.6.2             textshaping_0.3.7     fansi_1.0.6          
-##  [88] cytolib_2.15.2        ComplexHeatmap_2.19.0 dplyr_1.1.4          
-##  [91] Rgraphviz_2.47.0      gtable_0.3.4          sass_0.4.8           
-##  [94] digest_0.6.34         BiocGenerics_0.49.1   farver_2.1.1         
-##  [97] rjson_0.2.21          memoise_2.0.1         htmltools_0.5.7      
-## [100] pkgdown_2.0.7.9000    lifecycle_1.0.4       httr_1.4.7           
-## [103] GlobalOptions_0.1.2   bit64_4.0.5

+##  [88] cytolib_2.17.0        ComplexHeatmap_2.21.0 dplyr_1.1.4          
+##  [91] Rgraphviz_2.49.0      gtable_0.3.5          sass_0.4.9           
+##  [94] digest_0.6.35         BiocGenerics_0.51.0   farver_2.1.1         
+##  [97] rjson_0.2.21          htmlwidgets_1.6.4     memoise_2.0.1        
+## [100] htmltools_0.5.8.1     pkgdown_2.0.9.9000    lifecycle_1.0.4      
+## [103] httr_1.4.7            GlobalOptions_0.1.2   bit64_4.0.5

 

 

 
References
 

-

+

 

 Ellis B, Hahne F, Haaland P. 2022. flowCore: Basic Structures for Flow Cytometry
 Data. https://bioconductor.org/packages/flowCore/.
@@ -996,7 +988,7 @@ 
References
   

-
Site built with pkgdown 2.0.7.9000.

+
Site built with pkgdown 2.0.9.9000.

 

 
       
diff --git a/articles/CytoPipeline_files/figure-html/ggplotEvents1-1.png b/articles/CytoPipeline_files/figure-html/ggplotEvents1-1.png
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diff --git a/articles/CytoPipeline_files/figure-html/plotRetainedProp-1.png b/articles/CytoPipeline_files/figure-html/plotRetainedProp-1.png
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diff --git a/articles/CytoPipeline_files/figure-html/plotStepRemovedProp-1.png b/articles/CytoPipeline_files/figure-html/plotStepRemovedProp-1.png
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diff --git a/articles/Demo.html b/articles/Demo.html
index f4ac110..903ecb3 100644
--- a/articles/Demo.html
+++ b/articles/Demo.html
@@ -6,7 +6,7 @@
 
 
 Demonstration of the CytoPipeline R package suite functionalities • CytoPipeline
-
+
 
 
 
@@ -33,7 +33,7 @@
       
       
         CytoPipeline
-        1.3.6
+        1.5.1
       
     

 
@@ -166,9 +166,9 @@ 
Defining technical run parameters
 
Session information
 

-
## R Under development (unstable) (2024-02-19 r85946)
+
## R version 4.4.0 (2024-04-24)
 ## Platform: x86_64-pc-linux-gnu
-## Running under: Ubuntu 22.04.3 LTS
+## Running under: Ubuntu 22.04.4 LTS
 ## 
 ## Matrix products: default
 ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
@@ -189,21 +189,20 @@ 
Session information## [1] stats     graphics  grDevices utils     datasets  methods   base     
 ## 
 ## other attached packages:
-## [1] BiocStyle_2.31.0
+## [1] BiocStyle_2.33.0
 ## 
 ## loaded via a namespace (and not attached):
-##  [1] vctrs_0.6.5         cli_3.6.2           knitr_1.45         
-##  [4] rlang_1.1.3         xfun_0.42           stringi_1.8.3      
-##  [7] purrr_1.0.2         textshaping_0.3.7   jsonlite_1.8.8     
-## [10] glue_1.7.0          htmltools_0.5.7     ragg_1.2.7         
-## [13] sass_0.4.8          rmarkdown_2.25      evaluate_0.23      
-## [16] jquerylib_0.1.4     fastmap_1.1.1       yaml_2.3.8         
-## [19] lifecycle_1.0.4     memoise_2.0.1       bookdown_0.37      
-## [22] BiocManager_1.30.22 stringr_1.5.1       compiler_4.4.0     
-## [25] fs_1.6.3            systemfonts_1.0.5   digest_0.6.34      
-## [28] R6_2.5.1            magrittr_2.0.3      bslib_0.6.1        
-## [31] tools_4.4.0         pkgdown_2.0.7.9000  cachem_1.0.8       
-## [34] desc_1.4.3

+##  [1] vctrs_0.6.5         cli_3.6.2           knitr_1.46         
+##  [4] rlang_1.1.3         xfun_0.43           purrr_1.0.2        
+##  [7] textshaping_0.3.7   jsonlite_1.8.8      htmltools_0.5.8.1  
+## [10] ragg_1.3.1          sass_0.4.9          rmarkdown_2.26.2   
+## [13] evaluate_0.23       jquerylib_0.1.4     fastmap_1.1.1      
+## [16] yaml_2.3.8          lifecycle_1.0.4     memoise_2.0.1      
+## [19] bookdown_0.39       BiocManager_1.30.23 compiler_4.4.0     
+## [22] fs_1.6.4            htmlwidgets_1.6.4   systemfonts_1.0.6  
+## [25] digest_0.6.35       R6_2.5.1            magrittr_2.0.3     
+## [28] bslib_0.7.0         tools_4.4.0         pkgdown_2.0.9.9000 
+## [31] cachem_1.0.8        desc_1.4.3

 

   

 
@@ -224,7 +223,7 @@ 
Session information
   

-
Site built with pkgdown 2.0.7.9000.

+
Site built with pkgdown 2.0.9.9000.

 

 
       
diff --git a/articles/index.html b/articles/index.html
index f46c637..2f3ba66 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -1,5 +1,5 @@
 
-Articles • CytoPipelineArticles • CytoPipeline
@@ -17,7 +17,7 @@
       
       
         CytoPipeline
-        1.3.6
+        1.5.1
       
     

 
@@ -77,7 +77,7 @@ 
All vignettes

 

 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       

diff --git a/authors.html b/authors.html
index 8c2c556..38bc055 100644
--- a/authors.html
+++ b/authors.html
@@ -1,5 +1,5 @@
 
-Authors and Citation • CytoPipelineAuthors and Citation • CytoPipeline
@@ -17,7 +17,7 @@
       
       
         CytoPipeline
-        1.3.6
+        1.5.1
       
     

 
@@ -57,7 +57,7 @@
   

     

       

-        
Authors

+        
Authors and Citation

       

 
       
@@ -113,7 +113,7 @@ 
Citation

 

 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       

diff --git a/index.html b/index.html
index 4ab9406..a500d3c 100644
--- a/index.html
+++ b/index.html
@@ -6,7 +6,7 @@
 
 
 Automation and visualization of flow cytometry data analysis pipelines • CytoPipeline
-
+
 
 
 
@@ -33,7 +33,7 @@
       
       
         CytoPipeline
-        1.3.6
+        1.5.1
       
     

 
@@ -155,7 +155,7 @@ 
Developers

 
 

   

-
Site built with pkgdown 2.0.7.9000.

+
Site built with pkgdown 2.0.9.9000.

 

 
       
diff --git a/news/index.html b/news/index.html
index 95d001c..4c04625 100644
--- a/news/index.html
+++ b/news/index.html
@@ -1,5 +1,5 @@
 
-Changelog • CytoPipelineChangelog • CytoPipeline
@@ -17,7 +17,7 @@
       
       
         CytoPipeline
-        1.3.6
+        1.5.1
       
     

 
@@ -60,6 +60,14 @@ 
Changelog 

       Source: NEWS.md
     

 
+    

+
CytoPipeline 1.5

+

+
CytoPipeline 1.5.1

+
  • updated processing step argument matching using phenoData
+
    • 
+

+

     

 
CytoPipeline 1.3

 

@@ -185,7 +193,7 @@ 
CytoPipeline 0.99.0
-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       

diff --git a/pkgdown.yml b/pkgdown.yml
index bdaa920..8bd5cf1 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,8 +1,8 @@
-pandoc: 3.1.1
-pkgdown: 2.0.7.9000
-pkgdown_sha: 3979e7c0afbba4503248dc8a6d04fe0a2e03f26f
+pandoc: 3.1.13
+pkgdown: 2.0.9.9000
+pkgdown_sha: c76d8daed6ff2b57361747bd1795e0ea0a03b06b
 articles:
   CytoPipeline: CytoPipeline.html
   Demo: Demo.html
-last_built: 2024-02-23T15:08Z
+last_built: 2024-05-11T09:42Z
 
diff --git a/reference/CytoPipeline.html b/reference/CytoPipeline.html
index b97700a..74b7dff 100644
--- a/reference/CytoPipeline.html
+++ b/reference/CytoPipeline.html
@@ -1,5 +1,5 @@
 
-CytoPipeline package — CytoPipeline • CytoPipelineCytoPipeline package — CytoPipeline • CytoPipeline
         CytoPipeline
-        1.3.6
+        1.5.1
       
     

 
@@ -123,7 +123,7 @@ 
Author

 

 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       

diff --git a/reference/CytoPipelineClass.html b/reference/CytoPipelineClass.html
index 86a54d5..c92809a 100644
--- a/reference/CytoPipelineClass.html
+++ b/reference/CytoPipelineClass.html
@@ -1,5 +1,5 @@
 
-CytoPipeline class — CytoPipeline-class • CytoPipelineCytoPipeline class — CytoPipeline-class • CytoPipeline
         CytoPipeline
-        1.3.6
+        1.5.1
       
     

 
@@ -75,10 +75,10 @@ 
CytoPipeline class

 

 
     

-    
# S4 method for CytoPipeline
+    
# S4 method for class 'CytoPipeline'
 show(object)
 
-# S4 method for missing
+# S4 method for class 'missing'
 CytoPipeline(
   object,
   experimentName = "default_experiment",
@@ -86,7 +86,7 @@ 
CytoPipeline class

   pData = NULL
 )
 
-# S4 method for list
+# S4 method for class 'list'
 CytoPipeline(
   object,
   experimentName = "default_experiment",
@@ -94,7 +94,7 @@ 
CytoPipeline class

   pData = NULL
 )
 
-# S4 method for character
+# S4 method for class 'character'
 CytoPipeline(
   object,
   experimentName = "default_experiment",
@@ -102,7 +102,7 @@ 
CytoPipeline class

   pData = NULL
 )
 
-# S3 method for CytoPipeline
+# S3 method for class 'CytoPipeline'
 as.list(x, ...)
 
 experimentName(x)
@@ -120,31 +120,31 @@ 
CytoPipeline class

 
     

     
Arguments

-    
object

+    
object

 
a character() containing a JSON input

 
 
-
experimentName

+
experimentName

 
the experiment name

 
 
-
sampleFiles

+
sampleFiles

 
the sample files

 
 
-
pData

+
pData

 
the pheno Data (data.frame or NULL)

 
 
-
x

+
x

 
a CytoPipeline object

 
 
-
...

+
...

 
additional arguments (not used here)

 
 
-
value

+
value

 
the new value to be assigned

 
 

@@ -390,7 +390,7 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       

diff --git a/reference/CytoProcessingStep.html b/reference/CytoProcessingStep.html
index e7683a3..2ab440f 100644
--- a/reference/CytoProcessingStep.html
+++ b/reference/CytoProcessingStep.html
@@ -1,5 +1,5 @@
 
-Cyto Processing step — CytoProcessingStep • CytoPipelineCyto Processing step — CytoProcessingStep • CytoPipeline
         CytoPipeline
-        1.3.6
+        1.5.1
       
     

 
@@ -78,7 +78,7 @@ 
Cyto Processing step

     

     
CytoProcessingStep(name = character(), FUN = character(), ARGS = list())
 
-# S4 method for CytoProcessingStep
+# S4 method for class 'CytoProcessingStep'
 show(object)
 
 executeProcessingStep(x, ...)
@@ -89,7 +89,7 @@ 
Cyto Processing step

 
 getCPSARGS(x)
 
-# S3 method for CytoProcessingStep
+# S3 method for class 'CytoProcessingStep'
 as.list(x, ...)
 
 as.json.CytoProcessingStep(x, pretty = FALSE)
@@ -99,36 +99,36 @@ 
Cyto Processing step

 
     

     
Arguments

-    
name

+    
name

 
character denoting a name to the step, which can be different
 from the function name

 
 
-
FUN

+
FUN

 
function or character representing a function name.

 
 
-
ARGS

+
ARGS

 
list of arguments to be passed along to FUN.

 
 
-
object

+
object

 
a CytoProcessingStep object.

 
 
-
x

+
x

 
a CytoProcessingStep object.

 
 
-
...

+
...

 
other arguments (not used)

 
 
-
pretty

+
pretty

 
formatting set-up (see jsonlite::toJSON doc)

 
 
-
jsonString

+
jsonString

 
a character() containing a JSON string.

 
 

@@ -195,7 +195,7 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       

diff --git a/reference/OMIP021Samples.html b/reference/OMIP021Samples.html
index b87ff91..bc9277b 100644
--- a/reference/OMIP021Samples.html
+++ b/reference/OMIP021Samples.html
@@ -1,5 +1,5 @@
 
-OMIP021Samples dataset — OMIP021Samples • CytoPipelineOMIP021Samples dataset — OMIP021Samples • CytoPipeline
@@ -17,7 +17,7 @@
       
       
         CytoPipeline
-        1.3.6
+        1.5.1
       
     

 
@@ -96,7 +96,7 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       

diff --git a/reference/Rplot004.png b/reference/Rplot004.png
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index 90265e3..e22cbd1 100644
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index 93f9e9f..85f8c25 100644
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diff --git a/reference/Rplot016.png b/reference/Rplot016.png
index 318019d..56b5394 100644
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diff --git a/reference/Rplot017.png b/reference/Rplot017.png
index 79f6629..6beaf2c 100644
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diff --git a/reference/Rplot018.png b/reference/Rplot018.png
index c76a160..503a0d2 100644
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diff --git a/reference/aggregateAndSample.html b/reference/aggregateAndSample.html
index ad18fdc..cb58afd 100644
--- a/reference/aggregateAndSample.html
+++ b/reference/aggregateAndSample.html
@@ -1,5 +1,5 @@
 
-Aggregate and sample multiple flow frames of a flow set together — aggregateAndSample • CytoPipelineAggregate and sample multiple flow frames of a flow set together — aggregateAndSample • CytoPipeline
         CytoPipeline
-        1.3.6
+        1.5.1
       
     

 
@@ -95,35 +95,35 @@ 
Aggregate and sample multiple flow frames of a flow set together

 
     

     
Arguments

-    
fs

+    
fs

 
a flowCore::flowset

 
 
-
nTotalEvents

+
nTotalEvents

 
Total number of cells to select from the input flow
 frames

 
 
-
seed

+
seed

 
seed to be set before sampling for reproducibility.
 Default NULL does not set any seed.

 
 
-
channels

+
channels

 
Channels/markers to keep in the aggregate.
 Default NULL takes all channels of the first file.

 
 
-
writeOutput

+
writeOutput

 
Whether to write the resulting flowframe to a file.
 Default FALSE

 
 
-
outputFile

+
outputFile

 
Full path to output file. Default "aggregate.fcs"

 
 
-
keepOrder

+
keepOrder

 
If TRUE, the random subsample will be ordered in the same
 way as they were originally ordered in the file. Default = FALSE.

 
@@ -158,7 +158,7 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       

diff --git a/reference/appendCellID.html b/reference/appendCellID.html
index f48a4cd..3f2b2bf 100644
--- a/reference/appendCellID.html
+++ b/reference/appendCellID.html
@@ -1,5 +1,5 @@
 
-append 'Original_ID' column to a flowframe — appendCellID • CytoPipelineappend 'Original_ID' column to a flowframe — appendCellID • CytoPipelineapply scale transforms — applyScaleTransforms • CytoPipelineapply scale transforms — applyScaleTransforms • CytoPipeline
         CytoPipeline
-        1.3.6
+        1.5.1
       
     

 
@@ -79,19 +79,19 @@ 
apply scale transforms

 
     

     
Arguments

-    
x

+    
x

 
a flowCore::flowSet or a flowCore::flowFrame

 
 
-
transList

+
transList

 
a flowCore::transformList

 
 
-
verbose

+
verbose

 
if TRUE, send a message per flowFrame transformed

 
 
-
...

+
...

 
other arguments (not used)

 
 

@@ -115,7 +115,6 @@ 
Examples

 
 ff_c <- compensateFromMatrix(OMIP021Samples[[1]],
                              matrixSource = "fcs")  
-#> Compensating file : Donor1.fcs
 
 ff_t <- applyScaleTransforms(ff_c, transList = transList)
 
@@ -133,7 +132,7 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       

diff --git a/reference/areFluoCols.html b/reference/areFluoCols.html
index c9645f3..c75960d 100644
--- a/reference/areFluoCols.html
+++ b/reference/areFluoCols.html
@@ -1,5 +1,5 @@
 
-find flow frame columns that represent fluorochrome channel — areFluoCols • CytoPipelinefind flow frame columns that represent fluorochrome channel — areFluoCols • CytoPipeline
@@ -17,7 +17,7 @@
       
       
         CytoPipeline
-        1.3.6
+        1.5.1
       
     

 
@@ -74,11 +74,11 @@ 
find flow frame columns that represent fluorochrome channel

 
     

     
Arguments

-    
x

+    
x

 
a flowCore::flowFrame or a flowCore::flowSet

 
 
-
toRemovePatterns

+
toRemovePatterns

 
a vector of string patterns that are to be considered
 as non fluorochrome

 
@@ -122,7 +122,7 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       

diff --git a/reference/areSignalCols.html b/reference/areSignalCols.html
index 0041c86..ff4ccc6 100644
--- a/reference/areSignalCols.html
+++ b/reference/areSignalCols.html
@@ -1,5 +1,5 @@
 
-find flow frame columns that represent true signal — areSignalCols • CytoPipelinefind flow frame columns that represent true signal — areSignalCols • CytoPipeline
@@ -17,7 +17,7 @@
       
       
         CytoPipeline
-        1.3.6
+        1.5.1
       
     

 
@@ -74,11 +74,11 @@ 
find flow frame columns that represent true signal

 
     

     
Arguments

-    
x

+    
x

 
a flowCore::flowFrame or a flowCore::flowSet

 
 
-
toRemovePatterns

+
toRemovePatterns

 
a vector of string patterns that are to be considered
 as non signal

 
@@ -122,7 +122,7 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       

diff --git a/reference/compensateFromMatrix.html b/reference/compensateFromMatrix.html
index f879ba0..8824906 100644
--- a/reference/compensateFromMatrix.html
+++ b/reference/compensateFromMatrix.html
@@ -1,5 +1,5 @@
 
-compensation of fcs file(s) from matrix — compensateFromMatrix • CytoPipelinecompensation of fcs file(s) from matrix — compensateFromMatrix • CytoPipelinecompute linear transformation of scatter channels found in ff, based on 5% and 95% of referenceChannel, set as target. If there is a transformation defined in transList for referenceChannel, it is applied first, before computing quantiles. Then the computed linear transformations (or each scatter channel) are added into the transfo_list. -A channels are computed, and same linear transformation is then applied to corresponding -W and -H channels (if they exist in ff). — computeScatterChannelsLinearScale • CytoPipelinecompute linear transformation of scatter channels found in ff, based on 5% and 95% of referenceChannel, set as target. If there is a transformation defined in transList for referenceChannel, it is applied first, before computing quantiles. Then the computed linear transformations (or each scatter channel) are added into the transfo_list. -A channels are computed, and same linear transformation is then applied to corresponding -W and -H channels (if they exist in ff). — computeScatterChannelsLinearScale • CytoPipeline
@@ -17,7 +17,7 @@
       
       
         CytoPipeline
-        1.3.6
+        1.5.1
@@ -76,20 +76,20 @@

compute linear transformation of scatter channels found in ff, based on 5% a

Arguments

-
ff
+
ff

a flowCore::flowFrame

-
transList
+
transList

an initial flowCore::transformList

-
referenceChannel
+
referenceChannel

the reference channel to take target quantile values from. Can be defined as marker or channel name.

-
silent
+
silent

if FALSE, will output some information on the computed linear transformations

@@ -131,7 +131,7 @@

Examples

-

Site built with pkgdown 2.0.7.9000.

+

Site built with pkgdown 2.0.9.9000.

diff --git a/reference/estimateScaleTransforms.html b/reference/estimateScaleTransforms.html index 3bf2f05..0949e31 100644 --- a/reference/estimateScaleTransforms.html +++ b/reference/estimateScaleTransforms.html @@ -1,5 +1,5 @@ -estimates scale tranformations — estimateScaleTransforms • CytoPipelineestimates scale tranformations — estimateScaleTransforms • CytoPipeline CytoPipeline - 1.3.6 + 1.5.1

@@ -101,28 +101,28 @@

estimates scale tranformations

Arguments

-
ff
+
ff

a flowCore::flowFrame

-
fluoMethod
+
fluoMethod

method to be applied to all fluo channels

-
scatterMethod
+
scatterMethod

method to be applied to all scatter channels

-
scatterRefMarker
+
scatterRefMarker

the reference channel that is used to align the

-
specificScatterChannels
+
specificScatterChannels

vector of scatter channels for which we still want to apply the fluo method (and not the scatter Method)

-
verbose
+
verbose

if TRUE, send messages to the user at each step

@@ -162,7 +162,7 @@

Examples

-

Site built with pkgdown 2.0.7.9000.

+

Site built with pkgdown 2.0.9.9000.

diff --git a/reference/execute.html b/reference/execute.html index 76e8b3a..fb7e5fa 100644 --- a/reference/execute.html +++ b/reference/execute.html @@ -1,5 +1,5 @@ -executing CytoPipeline object — execute • CytoPipelineexecuting CytoPipeline object — execute • CytoPipeline CytoPipeline - 1.3.6 + 1.5.1 @@ -103,33 +103,33 @@

executing CytoPipeline object

Arguments

-
x
+
x

CytoPipeline object

-
path
+
path

base path, a subdirectory with name equal to the experiment will be created to store the output data, in particular the experiment cache

-
rmCache
+
rmCache

if TRUE, starts by removing the already existing cache directory corresponding to the experiment

-
useBiocParallel
+
useBiocParallel

if TRUE, use BiocParallel for computation of the sample file pre-processing in parallel (one file per worker at a time). Note the BiocParallel function used is bplapply()

-
BPPARAM
+
BPPARAM

if useBiocParallel is TRUE, sets the BPPARAM back-end to be used for the computation. If not provided, will use the top back-end on the BiocParallel::registered() stack.

-
BPOPTIONS
+
BPOPTIONS

if useBiocParallel is TRUE, sets the BPOPTIONS to be passed to bplapply() function. Note that if you use a SnowParams back-end, you need to specify all @@ -139,7 +139,7 @@

Arguments

(hence the default BPOPTIONS = bpoptions(packages = c("flowCore")) )

-
saveLastStepFF
+
saveLastStepFF

if TRUE, save the final result of the pre-processing, for each file. By convention, these output files are stored in @@ -148,21 +148,21 @@

Arguments

and with file extension corresponding to saveFFFormat.

-
saveFFSuffix
+
saveFFSuffix

FF file name suffix

-
saveFFFormat
+
saveFFFormat

either fcs or csv

-
saveFFCsvUseChannelMarker
+
saveFFCsvUseChannelMarker

if TRUE (default), converts the channels to the corresponding marker names (where the Marker is not NA). This setting is only applicable to export in csv format.

-
saveScaleTransforms
+
saveScaleTransforms

if TRUE (default FALSE), save on disk (in RDS format) the flowCore::transformList object obtained after running the scaleTransform processing queue. The file name is hardcoded to @@ -365,8 +365,6 @@

Examples

#> Removing margins from file : Donor1.fcs #> Removing margins from file : Donor2.fcs #> Proceeding with step 3 [compensate] ... -#> Compensating file : Donor1.fcs -#> Compensating file : Donor2.fcs #> Proceeding with step 4 [flowframe_aggregate] ... #> Proceeding with step 5 [scale_transform_estimate] ... #> ##################################################### @@ -376,7 +374,6 @@

Examples

#> Proceeding with step 2 [remove_margins] ... #> Removing margins from file : Donor1.fcs #> Proceeding with step 3 [compensate] ... -#> Compensating file : Donor1.fcs #> Proceeding with step 4 [remove_debris] ... #> Proceeding with step 5 [remove_dead_cells] ... #> Proceeding with step 6 [perform_QC] ... @@ -393,7 +390,6 @@

Examples

#> Proceeding with step 2 [remove_margins] ... #> Removing margins from file : Donor2.fcs #> Proceeding with step 3 [compensate] ... -#> Compensating file : Donor2.fcs #> Proceeding with step 4 [remove_debris] ... #> Proceeding with step 5 [remove_dead_cells] ... #> Proceeding with step 6 [perform_QC] ... @@ -455,8 +451,6 @@

Examples

#> Removing margins from file : Donor1.fcs #> Removing margins from file : Donor2.fcs #> Proceeding with step 3 [compensate] ... -#> Compensating file : Donor1.fcs -#> Compensating file : Donor2.fcs #> Proceeding with step 4 [flowframe_aggregate] ... #> Proceeding with step 5 [scale_transform_estimate] ... #> ##################################################### @@ -466,7 +460,6 @@

Examples

#> Proceeding with step 2 [remove_margins] ... #> Removing margins from file : Donor1.fcs #> Proceeding with step 3 [compensate] ... -#> Compensating file : Donor1.fcs #> Proceeding with step 4 [remove_doublets] ... #> Proceeding with step 5 [remove_debris] ... #> Proceeding with step 6 [remove_dead_cells] ... @@ -484,7 +477,6 @@

Examples

#> Proceeding with step 2 [remove_margins] ... #> Removing margins from file : Donor2.fcs #> Proceeding with step 3 [compensate] ... -#> Compensating file : Donor2.fcs #> Proceeding with step 4 [remove_doublets] ... #> Proceeding with step 5 [remove_debris] ... #> Proceeding with step 6 [remove_dead_cells] ... @@ -551,7 +543,7 @@

Examples

-

Site built with pkgdown 2.0.7.9000.

+

Site built with pkgdown 2.0.9.9000.

diff --git a/reference/exportCytoPipeline.html b/reference/exportCytoPipeline.html index 7330733..70efcb7 100644 --- a/reference/exportCytoPipeline.html +++ b/reference/exportCytoPipeline.html @@ -1,5 +1,5 @@ -exporting CytoPipeline objects — exportCytoPipeline • CytoPipelineexporting CytoPipeline objects — exportCytoPipeline • CytoPipelinefind time channel in flowSet/flowFrame — findTimeChannel • CytoPipelinefind time channel in flowSet/flowFrame — findTimeChannel • CytoPipelineextract compensation matrix from a flowCore::flowFrame — getAcquiredCompensationMatrix • CytoPipelineextract compensation matrix from a flowCore::flowFrame — getAcquiredCompensationMatrix • CytoPipelineget channel names from markers — getChannelNamesFromMarkers • CytoPipelineget channel names from markers — getChannelNamesFromMarkers • CytoPipeline @@ -17,7 +17,7 @@ CytoPipeline - 1.3.6 + 1.5.1 @@ -71,11 +71,11 @@

get channel names from markers

Arguments

-
ff
+
ff

a flowCore::flowFrame

-
markers
+
markers

a vector of markers, either provided as :

  • an array of booleans (referring to flowFrame columns)

  • an array of integers (indices in flowFrame columns)

  • an array of characters (exact markers or channel patterns)

    • @@ -142,7 +142,7 @@

    Examples

-

Site built with pkgdown 2.0.7.9000.

+

Site built with pkgdown 2.0.9.9000.

diff --git a/reference/getFCSFileName.html b/reference/getFCSFileName.html index 307d02e..b1a44eb 100644 --- a/reference/getFCSFileName.html +++ b/reference/getFCSFileName.html @@ -1,5 +1,5 @@ -get fcs file name — getFCSFileName • CytoPipelineget fcs file name — getFCSFileName • CytoPipeline @@ -17,7 +17,7 @@ CytoPipeline - 1.3.6 + 1.5.1 @@ -71,7 +71,7 @@

get fcs file name

Arguments

-
ff
+
ff

a flowCore::flowFrame

@@ -102,7 +102,7 @@

Examples

-

Site built with pkgdown 2.0.7.9000.

+

Site built with pkgdown 2.0.9.9000.

diff --git a/reference/getTransfoParams.html b/reference/getTransfoParams.html index 5c653f5..96e6664 100644 --- a/reference/getTransfoParams.html +++ b/reference/getTransfoParams.html @@ -1,5 +1,5 @@ -get tranformation parameters for a specific channel — getTransfoParams • CytoPipelineget tranformation parameters for a specific channel — getTransfoParams • CytoPipelineplot events in 1D or 2D, using ggplot2 — ggplotEvents • CytoPipelineplot events in 1D or 2D, using ggplot2 — ggplotEvents • CytoPipeline CytoPipeline - 1.3.6 + 1.5.1 @@ -96,78 +96,78 @@

plot events in 1D or 2D, using ggplot2

Arguments

-
obj
+
obj

a flowCore::flowFrame or flowCore::flowSet

-
xChannel
+
xChannel

channel (name or index) or marker name to be displayed on x axis

-
yChannel
+
yChannel

channel (name or index) or marker name to be displayed on y axis

-
nDisplayCells
+
nDisplayCells

maximum number of events that will be plotted. If the number of events exceed this number, a sub-sampling will be performed

-
seed
+
seed

seed used for sub-sampling (if any)

-
bins
+
bins

used in geom_hex

-
fill
+
fill

used in geom_density

-
alpha
+
alpha

used in geom_density

-
xScale
+
xScale

scale to be used for the x axis (note "linear" corresponds to no transformation)

-
yScale
+
yScale

scale to be used for the y axis (note "linear" corresponds to no transformation)

-
xLogicleParams
+
xLogicleParams

if (xScale == "logicle"), the parameters of the logicle transformation to be used, as a list(w = ..., m = ..., a = ..., t = ...). If NULL, these parameters will be estimated by flowCore::estimateLogicle()

-
yLogicleParams
+
yLogicleParams

if (yScale == "logicle"), the parameters of the logicle transformation to be used, as a list(w = ..., m = ..., a = ..., t = ...). If NULL, these parameters will be estimated by flowCore::estimateLogicle()

-
xLinearRange
+
xLinearRange

if (xScale == "linear"), the x axis range to be used

-
yLinearRange
+
yLinearRange

if (yScale == "linear"), the y axis range to be used

-
transList
+
transList

optional list of scale transformations to be applied to each channel. If it is non null, 'x/yScale', 'x/yLogicleParams' and 'x/yLinear_range' will be discarded.

-
runTransforms
+
runTransforms

(TRUE/FALSE) Will the application of non linear scale result in data being effectively transformed ?

  • If TRUE, than the data will undergo transformations prior to visualization.

    • @@ -362,7 +362,7 @@

    Examples

-

Site built with pkgdown 2.0.7.9000.

+

Site built with pkgdown 2.0.9.9000.

diff --git a/reference/ggplotFilterEvents-1.png b/reference/ggplotFilterEvents-1.png index 1023bfe..7ff4ec6 100644 Binary files a/reference/ggplotFilterEvents-1.png and b/reference/ggplotFilterEvents-1.png differ diff --git a/reference/ggplotFilterEvents-2.png b/reference/ggplotFilterEvents-2.png index 961b7d3..50fa433 100644 Binary files a/reference/ggplotFilterEvents-2.png and b/reference/ggplotFilterEvents-2.png differ diff --git a/reference/ggplotFilterEvents.html b/reference/ggplotFilterEvents.html index 57dc76d..f3ccf34 100644 --- a/reference/ggplotFilterEvents.html +++ b/reference/ggplotFilterEvents.html @@ -1,5 +1,5 @@ -plot filtered events in 2D, using ggplot — ggplotFilterEvents • CytoPipelineplot filtered events in 2D, using ggplot — ggplotFilterEvents • CytoPipeline CytoPipeline - 1.3.6 + 1.5.1 @@ -97,74 +97,74 @@

plot filtered events in 2D, using ggplot

Arguments

-
ffPre
+
ffPre

a flowCore::flowFrame, before applying filter

-
ffPost
+
ffPost

a flowCore::flowFrame, after applying filter

-
xChannel
+
xChannel

channel (name or index) or marker name to be displayed on x axis

-
yChannel
+
yChannel

channel (name or index) or marker name to be displayed on y axis

-
nDisplayCells
+
nDisplayCells

maximum number of events that will be plotted. If the number of events exceed this number, a subsampling will be performed

-
seed
+
seed

seed used for sub-sampling (if any)

-
size
+
size

used by geom_point()

-
xScale
+
xScale

scale to be used for the x axis (note "linear" corresponds to no transformation)

-
yScale
+
yScale

scale to be used for the y axis (note "linear" corresponds to no transformation)

-
xLogicleParams
+
xLogicleParams

if (xScale == "logicle"), the parameters of the logicle transformation to be used, as a list(w = ..., m = ..., a = ..., t = ...) If NULL, these parameters will be estimated by flowCore::estimateLogicle()

-
yLogicleParams
+
yLogicleParams

if (yScale == "logicle"), the parameters of the logicle transformation to be used, as a list(w = ..., m = ..., a = ..., t = ...) If NULL, these parameters will be estimated by flowCore::estimateLogicle()

-
xLinearRange
+
xLinearRange

if (xScale == "linear"), linear range to be used

-
yLinearRange
+
yLinearRange

if (yScale == "linear"), linear range to be used

-
transList
+
transList

optional list of scale transformations to be applied to each channel. If it is non null, 'x/yScale', 'x/yLogicleParams' and 'x/yLinear_range' will be discarded.

-
runTransforms
+
runTransforms

(TRUE/FALSE) Will the application of non linear scale result in data being effectively transformed ?

  • If TRUE, than the data will undergo transformations prior to visualization.

    • @@ -173,7 +173,7 @@

    Arguments

-
interactive
+
interactive

if TRUE, transform the scaling formats such that the ggcyto::x_scale_logicle() and ggcyto::y_scale_logicle() do work with plotly::ggplotly()

@@ -260,7 +260,7 @@

Examples

-

Site built with pkgdown 2.0.7.9000.

+

Site built with pkgdown 2.0.9.9000.

diff --git a/reference/ggplotFlowRate-1.png b/reference/ggplotFlowRate-1.png index ab53db5..86552e2 100644 Binary files a/reference/ggplotFlowRate-1.png and b/reference/ggplotFlowRate-1.png differ diff --git a/reference/ggplotFlowRate-2.png b/reference/ggplotFlowRate-2.png index 8f183ce..deb61f2 100644 Binary files a/reference/ggplotFlowRate-2.png and b/reference/ggplotFlowRate-2.png differ diff --git a/reference/ggplotFlowRate-3.png b/reference/ggplotFlowRate-3.png index d9fdbfa..4186b7b 100644 Binary files a/reference/ggplotFlowRate-3.png and b/reference/ggplotFlowRate-3.png differ diff --git a/reference/ggplotFlowRate-4.png b/reference/ggplotFlowRate-4.png index 40733c9..38b2bb9 100644 Binary files a/reference/ggplotFlowRate-4.png and b/reference/ggplotFlowRate-4.png differ diff --git a/reference/ggplotFlowRate.html b/reference/ggplotFlowRate.html index 06cc651..c858241 100644 --- a/reference/ggplotFlowRate.html +++ b/reference/ggplotFlowRate.html @@ -1,5 +1,5 @@ -plot flow rate as a function of time, using ggplot2 — ggplotFlowRate • CytoPipelineplot flow rate as a function of time, using ggplot2 — ggplotFlowRate • CytoPipeline @@ -17,7 +17,7 @@ CytoPipeline - 1.3.6 + 1.5.1 @@ -71,15 +71,15 @@

plot flow rate as a function of time, using ggplot2

Arguments

-
obj
+
obj

a flowCore::flowFrame or flowCore::flowSet

-
title
+
title

a title for the graph

-
timeUnit
+
timeUnit

which time interval is used to calculate "instant" flow rate (default = 100 ms)

@@ -126,7 +126,7 @@

Examples

-

Site built with pkgdown 2.0.7.9000.

+

Site built with pkgdown 2.0.9.9000.

diff --git a/reference/handlingProcessingSteps.html b/reference/handlingProcessingSteps.html index 1a1558a..836ed6f 100644 --- a/reference/handlingProcessingSteps.html +++ b/reference/handlingProcessingSteps.html @@ -1,5 +1,5 @@ -handling processing steps in CytoPipeline objects — handlingProcessingSteps • CytoPipelinehandling processing steps in CytoPipeline objects — handlingProcessingSteps • CytoPipelineFunction reference • CytoPipelinePackage index • CytoPipeline @@ -17,7 +17,7 @@ CytoPipeline - 1.3.6 + 1.5.1 @@ -232,7 +232,7 @@

All functions
-

Site built with pkgdown 2.0.7.9000.

+

Site built with pkgdown 2.0.9.9000.

diff --git a/reference/inspectCytoPipelineObjects.html b/reference/inspectCytoPipelineObjects.html index bce7488..5d3c051 100644 --- a/reference/inspectCytoPipelineObjects.html +++ b/reference/inspectCytoPipelineObjects.html @@ -1,5 +1,5 @@ -inspect CytoPipeline results objects — inspectCytoPipelineObjects • CytoPipelineinspect CytoPipeline results objects — inspectCytoPipelineObjects • CytoPipelineinteraction between CytoPipeline object and disk cache — interactingWithCytoPipelineCache • CytoPipelineinteraction between CytoPipeline object and disk cache — interactingWithCytoPipelineCache • CytoPipelineperform QC with flowAI — qualityControlFlowAI • CytoPipelineperform QC with flowAI — qualityControlFlowAI • CytoPipelineperform QC with PeacoQC — qualityControlPeacoQC • CytoPipelineperform QC with PeacoQC — qualityControlPeacoQC • CytoPipelineread RDS object — readRDSObject • CytoPipelineread RDS object — readRDSObject • CytoPipelineRead fcs sample files — readSampleFiles • CytoPipelineremove channels from a flowFrame — removeChannels • CytoPipelineremove channels from a flowFrame — removeChannels • CytoPipelineremove dead cells from a flowFrame using manual gating — removeDeadCellsManualGate • CytoPipelineremove dead cells from a flowFrame using manual gating — removeDeadCellsManualGate • CytoPipelineremove debris from a flowFrame using manual gating — removeDebrisManualGate • CytoPipelineremove debris from a flowFrame using manual gating — removeDebrisManualGate • CytoPipelineremove doublets from a flowFrame, using CytoPipeline custom algorithm — removeDoubletsCytoPipeline • CytoPipelineremove doublets from a flowFrame, using CytoPipeline custom algorithm — removeDoubletsCytoPipeline • CytoPipelineremove margin events using PeacoQC — removeMarginsPeacoQC • CytoPipelineremove margin events using PeacoQC — removeMarginsPeacoQC • CytoPipelinereset 'Original_ID' column in a flowframe — resetCellIDs • CytoPipelinereset 'Original_ID' column in a flowframe — resetCellIDs • CytoPipeline CytoPipeline - 1.3.6 + 1.5.1 @@ -79,11 +79,11 @@

reset 'Original_ID' column in a flowframe

Arguments

-
ff
+
ff

a flowCore::flowFrame

-
eventIDs
+
eventIDs

an integer vector containing the values to be set in expression matrix, as Original ID's.

@@ -122,7 +122,7 @@

Examples

-

Site built with pkgdown 2.0.7.9000.

+

Site built with pkgdown 2.0.9.9000.

diff --git a/reference/runCompensation.html b/reference/runCompensation.html index 859dd5d..91c2f51 100644 --- a/reference/runCompensation.html +++ b/reference/runCompensation.html @@ -1,5 +1,5 @@ -compensate with additional options — runCompensation • CytoPipelinecompensate with additional options — runCompensation • CytoPipelineClean doublet events from flow cytometry data — singletsGate • CytoPipelineClean doublet events from flow cytometry data — singletsGate • CytoPipeline CytoPipeline - 1.3.6 + 1.5.1 @@ -94,31 +94,31 @@

Clean doublet events from flow cytometry data

Arguments

-
ff
+
ff

A flowCore::flowframe that contains flow cytometry data.

-
filterId
+
filterId

the name for the filter that is returned

-
channel1
+
channel1

The first channel that will be used to determine the doublet events. Default is "FSC-A"

-
channel2
+
channel2

The second channels that will be used to determine the doublet events. Default is "FSC-H"

-
nmad
+
nmad

Bandwidth above the ratio allowed (cells are kept if their ratio is smaller than the median ratio + nmad times the median absolute deviation of the ratios). Default is 4.

-
verbose
+
verbose

If set to TRUE, the median ratio and width will be printed. Default is FALSE.

@@ -199,7 +199,7 @@

Examples

-

Site built with pkgdown 2.0.7.9000.

+

Site built with pkgdown 2.0.9.9000.

diff --git a/reference/subsample.html b/reference/subsample.html index 432d566..a021ccc 100644 --- a/reference/subsample.html +++ b/reference/subsample.html @@ -1,5 +1,5 @@ -sub-sampling of a flowFrame — subsample • CytoPipelinesub-sampling of a flowFrame — subsample • CytoPipelineupdate marker name of a given flowFrame channel — updateMarkerName • CytoPipelineupdate marker name of a given flowFrame channel — updateMarkerName • CytoPipelinewrite flowFrame to disk — writeFlowFrame • CytoPipelinewrite flowFrame to disk — writeFlowFrame • CytoPipeline