Merge pull request #54 from ImmuneDynamics/development

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ImmuneDynamics · Jun 18, 2021 · cb54040 · cb54040
2 parents 88123c0 + 72a5f71
commit cb54040
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,16 +1,29 @@
 Package: Spectre
 Type: Package
-Title: A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data. 
-Version: 0.5.1
-Author: Thomas Ashhurst, Felix Marsh-Wakefield, Givanna Putri
-Maintainer: Thomas Ashhurst <[email protected]>
+Version: 0.5.2
+Date: 2021-06-18
+Title: High-dimensional cytometry and imaging analysis. 
 Description: A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data. 
+Authors@R: c(
+  person(given = "Thomas", family = "Ashhurst", email = "[email protected]", role = c("aut", "cre")),
+  person(given = "Felix", family = "Marsh-Wakefield", email = "[email protected]", role = "aut"),
+  person(given = "Givanna", family = "Putri", email = "[email protected]", role = "aut")
+  )
+URL: https://github.com/ImmuneDynamics/Spectre
+BugReports: https://github.com/ImmuneDynamics/Spectre/issues
+Maintainer: Thomas Ashhurst <[email protected]>
 Depends: R (>= 3.6.0)
 License: MIT Licence
 Encoding: UTF-8
 LazyData: true
+biocViews: flowCore
 Imports:
+    flowCore,
+    Biobase,
+    flowViz,
+    FlowSOM,
     devtools,
+    BiocManager,
     plyr,
     dplyr,
     data.table,
@@ -48,6 +61,5 @@ Imports:
     qs,
     s2,
     exactextractr,
-Suggests:
 RoxygenNote: 7.1.1
 Roxygen: list(markdown = TRUE)
diff --git a/NAMESPACE b/NAMESPACE
@@ -12,8 +12,8 @@ export(do.align)
 export(do.asinh)
 export(do.calculate.area)
 export(do.clip)
-export(do.create.outlines)
 export(do.combine.cols)
+export(do.create.outlines)
 export(do.embed.columns)
 export(do.extract)
 export(do.extract.cell.dat)

diff --git a/R/package.check.R b/R/package.check.R
@@ -19,39 +19,176 @@
 
 package.check <- function(type = "general"){
 
-    if(!is.element('data.table', installed.packages()[,1])) message('data.table is required but not installed')
-    if(!is.element('plyr', installed.packages()[,1])) message('plyr is required but not installed')
-    if(!is.element('dplyr', installed.packages()[,1])) message('dplyr is required but not installed')
-    if(!is.element('tidyr', installed.packages()[,1])) message('tidyr is required but not installed')
-    if(!is.element('rstudioapi', installed.packages()[,1])) message('rstudioapi is required but not installed')
-    if(!is.element('Rtsne', installed.packages()[,1])) message('Rtsne is required but not installed')
-    if(!is.element('umap', installed.packages()[,1])) message('umap is required but not installed')
-    if(!is.element('reticulate', installed.packages()[,1])) message('reticulate is required but not installed')
-    if(!is.element('ggplot2', installed.packages()[,1])) message('ggplot2 is required but not installed')
-    if(!is.element('ggthemes', installed.packages()[,1])) message('ggthemes is required but not installed')
-    if(!is.element('scales', installed.packages()[,1])) message('scales is required but not installed')
-    if(!is.element('colorRamps', installed.packages()[,1])) message('colorRamps is required but not installed')
-    if(!is.element('RColorBrewer', installed.packages()[,1])) message('RColorBrewer is required but not installed')
-    if(!is.element('gridExtra', installed.packages()[,1])) message('gridExtra is required but not installed')
-    if(!is.element('ggpointdensity', installed.packages()[,1])) message('ggpointdensity is required but not installed')
-    if(!is.element('pheatmap', installed.packages()[,1])) message('ggpointdensity is required but not installed')
-    if(!is.element('ggpubr', installed.packages()[,1])) message('ggpointdensity is required but not installed')
-    if(!is.element('caret', installed.packages()[,1])) message('caret is required for machine learning analysis but is not installed')
-    if(!is.element('class', installed.packages()[,1])) message('class is required for machine learning analysis but is not installed')
+    res.list <- list()
 
-    if(!is.element('flowCore', installed.packages()[,1])) message('flowCore is required but not installed. Please install from BioConductor.')
-    if(!is.element('Biobase', installed.packages()[,1])) message('Biobase is required but not installed. Please install from BioConductor.')
-    if(!is.element('flowViz', installed.packages()[,1])) message('flowViz is required but not installed. Please install from BioConductor.')
-    if(!is.element('FlowSOM', installed.packages()[,1])) message('FlowSOM is required but not installed. Please install from BioConductor.')
+    if(!is.element('data.table', installed.packages()[,1])){
+      message('data.table is required but not installed')
+      res.list[['data.table']] <- 'data.table'
+    } 
+
+    if(!is.element('plyr', installed.packages()[,1])) {
+      message('plyr is required but not installed')
+      res.list[['plyr']] <- 'plyr'
+    } 
+
+    if(!is.element('dplyr', installed.packages()[,1])) {
+      message('dplyr is required but not installed')
+      res.list[['data.table']] <- 'data.table'
+    } 
+
+    if(!is.element('tidyr', installed.packages()[,1])) {
+      message('tidyr is required but not installed')
+      res.list[['tidyr']] <- 'tidyr'
+    } 
+
+    if(!is.element('rstudioapi', installed.packages()[,1])) {
+      message('rstudioapi is required but not installed')
+      res.list[['rstudioapi']] <- 'rstudioapi'
+    } 
+
+    if(!is.element('Rtsne', installed.packages()[,1])) {
+      message('Rtsne is required but not installed')
+      res.list[['Rtsne']] <- 'Rtsne'
+    } 
+
+    if(!is.element('umap', installed.packages()[,1])) {
+      message('umap is required but not installed')
+      res.list[['umap']] <- 'umap'
+    } 
+
+    if(!is.element('reticulate', installed.packages()[,1])) {
+      message('reticulate is required but not installed')
+      res.list[['reticulate']] <- 'reticulate'
+    } 
+
+    if(!is.element('ggplot2', installed.packages()[,1])) {
+      message('ggplot2 is required but not installed')
+      res.list[['ggplot2']] <- 'ggplot2'
+    } 
+
+    if(!is.element('ggthemes', installed.packages()[,1])) {
+      message('ggthemes is required but not installed')
+      res.list[['ggthemes']] <- 'ggthemes'
+    } 
+
+    if(!is.element('scales', installed.packages()[,1])) {
+      message('scales is required but not installed')
+      res.list[['scales']] <- 'scales'
+    } 
+
+    if(!is.element('colorRamps', installed.packages()[,1])) {
+      message('colorRamps is required but not installed')
+      res.list[['colorRamps']] <- 'colorRamps'
+    } 
+
+    if(!is.element('RColorBrewer', installed.packages()[,1])) {
+      message('RColorBrewer is required but not installed')
+      res.list[['RColorBrewer']] <- 'RColorBrewer'
+    } 
+
+    if(!is.element('gridExtra', installed.packages()[,1])) {
+      message('gridExtra is required but not installed')
+      res.list[['gridExtra']] <- 'gridExtra'
+    } 
+
+    if(!is.element('ggpointdensity', installed.packages()[,1])) {
+      message('ggpointdensity is required but not installed')
+      res.list[['ggpointdensity']] <- 'ggpointdensity'
+    } 
+
+    if(!is.element('pheatmap', installed.packages()[,1])) {
+      message('pheatmap is required but not installed')
+      res.list[['pheatmap']] <- 'pheatmap'
+    } 
+
+    if(!is.element('ggpubr', installed.packages()[,1])) {
+      message('ggpubr is required but not installed')
+      res.list[['ggpubr']] <- 'ggpubr'
+    } 
+
+    if(!is.element('caret', installed.packages()[,1])) {
+      message('caret is required for machine learning analysis but is not installed')
+      res.list[['caret']] <- 'caret'
+    } 
+
+    if(!is.element('class', installed.packages()[,1])) {
+      message('class is required for machine learning analysis but is not installed')
+      res.list[['class']] <- 'class'
+    } 
+
+    if(!is.element('flowCore', installed.packages()[,1])) {
+      message('flowCore is required but not installed. Please install from BioConductor.')
+      res.list[['flowCore']] <- 'flowCore'
+    } 
+
+    if(!is.element('Biobase', installed.packages()[,1])) {
+      message('Biobase is required but not installed. Please install from BioConductor.')
+      res.list[['Biobase']] <- 'Biobase'
+    } 
+
+    if(!is.element('flowViz', installed.packages()[,1])) {
+      message('flowViz is required but not installed. Please install from BioConductor.')
+      res.list[['flowViz']] <- 'flowViz'
+    } 
+
+    if(!is.element('FlowSOM', installed.packages()[,1])) {
+      message('FlowSOM is required but not installed. Please install from BioConductor.')
+      res.list[['FlowSOM']] <- 'FlowSOM'
+    } 
+
 
   if(type == "spatial"){
-    if(!is.element('raster', installed.packages()[,1])) message('raster is required for SPATIAL analysis but is not installed')
-    if(!is.element('tiff', installed.packages()[,1])) message('tiff is required for SPATIAL analysis but is not installed')
-    if(!is.element('rgeos', installed.packages()[,1])) message('rgeos is required for SPATIAL analysis but is not installed')
-    if(!is.element('exactextractr', installed.packages()[,1])) message('exactextractr is required for SPATIAL analysis but is not installed')
-    if(!is.element('sp', installed.packages()[,1])) message('sp is required for SPATIAL analysis but is not installed')
-    if(!is.element('sf', installed.packages()[,1])) message('sf is required for SPATIAL analysis but is not installed')
-    if(!is.element('stars', installed.packages()[,1])) message('stars is required for SPATIAL analysis but is not installed')
-    if(!is.element('qs', installed.packages()[,1])) message('qs is required for SPATIAL analysis but is not installed')
+    if(!is.element('raster', installed.packages()[,1])) {
+      message('raster is required for SPATIAL analysis but is not installed')
+      res.list[['raster']] <- 'raster'
+    } 
+
+    if(!is.element('tiff', installed.packages()[,1])) {
+      message('tiff is required for SPATIAL analysis but is not installed')
+      res.list[['tiff']] <- 'tiff'
+    } 
+
+    if(!is.element('rgeos', installed.packages()[,1])) {
+      message('rgeos is required for SPATIAL analysis but is not installed')
+      res.list[['rgeos']] <- 'rgeos'
+    } 
+
+    if(!is.element('exactextractr', installed.packages()[,1])) {
+      message('exactextractr is required for SPATIAL analysis but is not installed')
+      res.list[['exactextractr']] <- 'exactextractr'
+    } 
+
+    if(!is.element('sp', installed.packages()[,1])) {
+      message('sp is required for SPATIAL analysis but is not installed')
+      res.list[['sp']] <- 'sp'
+    } 
+
+    if(!is.element('sf', installed.packages()[,1])) {
+      message('sf is required for SPATIAL analysis but is not installed')
+      res.list[['sf']] <- 'sf'
+    } 
+
+    if(!is.element('stars', installed.packages()[,1])) {
+      message('stars is required for SPATIAL analysis but is not installed')
+      res.list[['stars']] <- 'stars'
+    } 
+
+    if(!is.element('qs', installed.packages()[,1])) {
+      message('qs is required for SPATIAL analysis but is not installed')
+      res.list[['qs']] <- 'qs'
+    } 
+
+    if(!is.element('s2', installed.packages()[,1])) {
+      message('s2 is required for SPATIAL analysis but is not installed')
+      res.list[['s2']] <- 's2'
+    } 
   }
+
+
+  ### Final message
+
+    if(length(res.list) == 0){
+      message("All packages successfully installed")
+    }
+
 }