Update

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: Spectre
 Type: Package
-Title: A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry data. 
-Version: 0.4.5
+Title: A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data. 
+Version: 0.5.0
 Author: Thomas Ashhurst, Felix Marsh-Wakefield, Givanna Putri
 Maintainer: Thomas Ashhurst <thomas.ashhurst@sydney.edu.au>
 Description: A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry data. 
@@ -36,7 +36,17 @@ Imports:
     ggraph,
     stringr,
     rsvd,
-    irlba
+    irlba,
+    gridExtra,
+    raster,
+    tiff,
+    rgeos,
+    tidyr,
+    sp,
+    sf,
+    stars,
+    qs,
+    exactextractr
 Suggests:
 RoxygenNote: 7.1.1
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -5,17 +5,26 @@ export(create.dt)
 export(create.stats)
 export(create.sumtable)
 export(do.add.cols)
+export(do.add.masks)
+export(do.add.percell)
 export(do.aggregate)
 export(do.align)
 export(do.asinh)
+export(do.calculate.area)
 export(do.clip)
+export(do.create.outlines)
 export(do.combine.cols)
 export(do.embed.columns)
+export(do.extract)
+export(do.extract.cell.dat)
 export(do.filter)
+export(do.filter.percell)
+export(do.label.from.polygon)
 export(do.list.summary)
 export(do.list.switch)
 export(do.logicle)
 export(do.merge.files)
+export(do.pull.data)
 export(do.reorder)
 export(do.rescale)
 export(do.stats)
@@ -27,12 +36,14 @@ export(make.colour.plot)
 export(make.multi.plot)
 export(make.network.plot)
 export(make.pheatmap)
+export(make.spatial.plot)
 export(make.volcano.plot)
 export(package.check)
 export(package.install)
 export(package.load)
 export(prep.cytonorm)
 export(read.files)
+export(read.spatial.files)
 export(run.align)
 export(run.chronoclust)
 export(run.cytonorm)
@@ -44,10 +55,12 @@ export(run.pca)
 export(run.phenograph)
 export(run.prepare.chronoclust)
 export(run.ruv)
+export(run.spatial.analysis)
 export(run.tsne)
 export(run.umap)
 export(train.cytonorm)
 export(train.knn.classifier)
 export(write.files)
+export(write.hdf5)
 export(write.sumtables)
 import(data.table)

R/create.dt.R

@@ -7,8 +7,7 @@
 #' 
 #' @usage create.dt(dat, from)
 #'
-#' @author
-#' Thomas M Ashhurst, \email{thomas.ashhurst@@sydney.edu.au}
+#' @author Thomas M Ashhurst, \email{thomas.ashhurst@@sydney.edu.au}
 #'
 #' @references \url{https://github.com/ImmuneDynamics/Spectre}.
 #' 

R/create.stats.R

@@ -11,6 +11,10 @@
 #' @param pairwise.test DEFAULT = 'wilcox.test'. Currently the only option
 #' @param corrections DEFAULT = 'fdr' (false discovery rate). Currently the only option
 #'
+#' @author Thomas M Ashhurst, \email{thomas.ashhurst@@sydney.edu.au}
+#'
+#' @references \url{https://github.com/ImmuneDynamics/Spectre}.
+#'
 #' @import data.table
 #'
 #' @export

R/create.sumtable.R

@@ -26,10 +26,9 @@
 #'                             use.cols = names(dat)[c(11:19)],
 #'                             counts = counts)
 #' 
-#' @author
-#' Thomas M Ashhurst, \email{thomas.ashhurst@@sydney.edu.au}
+#' @author Thomas M Ashhurst, \email{thomas.ashhurst@@sydney.edu.au}
 #'
-#' @references \url{https://sydneycytometry.org.au/spectre}.
+#' @references \url{https://github.com/ImmuneDynamics/Spectre}.
 #' 
 #' @export
 

R/demo.asinh.R

@@ -8,9 +8,9 @@
 #'
 #' @author Thomas M Ashhurst, \email{thomas.ashhurst@@sydney.edu.au}
 #'
-#' @source Thomas M Ashhurst.
+#' @references \url{https://github.com/ImmuneDynamics/Spectre}.
 #'
-#' @references \url{https://sydneycytometry.org.au/spectre}.
+#' @source Thomas M Ashhurst.
 #'
 #' @examples
 #' demo.asinh

R/demo.batches.1.R

@@ -10,7 +10,7 @@
 #'
 #' @source Thomas M Ashhurst.
 #'
-#' @references \url{https://sydneycytometry.org.au/spectre}.
+#' @references \url{https://github.com/ImmuneDynamics/Spectre}.
 #'
 #' @examples
 #' demo.batches.1

R/demo.clustered.R

@@ -10,8 +10,8 @@
 #'
 #' @source Thomas M Ashhurst.
 #'
-#' @references \url{https://sydneycytometry.org.au/spectre}.
-#'
+#' @references \url{https://github.com/ImmuneDynamics/Spectre}.
+#' 
 #' @examples
 #' demo.clustered
 #'

R/demo.exp.R

@@ -10,8 +10,8 @@
 #'
 #' @source Thomas M Ashhurst.
 #'
-#' @references \url{https://sydneycytometry.org.au/spectre}.
-#'
+#' @references \url{https://github.com/ImmuneDynamics/Spectre}.
+#' 
 #' @examples
 #' demo.exp
 #'

R/demo.spatial.R

@@ -0,0 +1,18 @@
+#' demo.spatial - Demo spatial dataset consisting of 6x regions of interest, acquired using Imaging Mass Cytometry  (IMC)
+#'
+#' @docType data
+#'
+#' @usage demo.spatial
+#'
+#' @format An R object (list) containing 6x ROIs, each consisting of raster stacks, masks, and extracted cellular data in a data.table
+#'
+#' @author Thomas M Ashhurst, \email{thomas.ashhurst@@sydney.edu.au}
+#'
+#' @source Thomas M Ashhurst.
+#' 
+#' @references \url{https://github.com/ImmuneDynamics/Spectre}.
+#' 
+#' @examples
+#' demo.spatial
+#'
+"demo.spatial"

R/demo.start.R

@@ -10,8 +10,8 @@
 #'
 #' @source Thomas M Ashhurst.
 #'
-#' @references \url{https://sydneycytometry.org.au/spectre}.
-#'
+#' @references \url{https://github.com/ImmuneDynamics/Spectre}.
+#' 
 #' @examples
 #' demo.start
 #'

R/demo.sum.R

@@ -10,8 +10,8 @@
 #'
 #' @source Thomas M Ashhurst.
 #'
-#' @references \url{https://sydneycytometry.org.au/spectre}.
-#'
+#' @references \url{https://github.com/ImmuneDynamics/Spectre}.
+#' 
 #' @examples
 #' demo.sum
 #'

R/do.add.cols.R

@@ -13,8 +13,8 @@
 #'
 #' @author Thomas M Ashhurst, \email{thomas.ashhurst@@sydney.edu.au}
 #'
-#' @references \url{https://sydneycytometry.org.au/spectre}.
-#'
+#' @references \url{https://github.com/ImmuneDynamics/Spectre}.
+#' 
 #' @examples
 #' add.dt <- data.table('Files' = unique(Spectre::demo.asinh$FileName),
 #'                      'SampleNumber' = c(1:12))

R/do.add.masks.R

@@ -0,0 +1,129 @@
+#' do.add.masks
+#'
+#' @param spatial.dat NO DEFAULT. Spatial data list.
+#' @param mask.loc NO DEFAULT. Directory of mask files.
+#' @param masks NO DEFAULT. Vector of mask file names
+#' @param mask.label DEFAULT = "cell_mask"
+#' @param mask.ext DEFAULT  = "_mask.tif" (will also recognise the '.tiff' file type)
+#' @param correct.extent DEFAULT = TRUE
+#' @param flip.y DEFAULT = TRUE
+#' @param value.modifier DEFAULT = 65535
+#' @param array DEFAULT = FALSE
+#'
+#' @author Thomas M Ashhurst, \email{thomas.ashhurst@@sydney.edu.au}
+#'
+#' @references \url{https://github.com/ImmuneDynamics/Spectre}.
+#'
+#' @import data.table
+#'
+#' @export
+
+do.add.masks <- function(spatial.dat,
+                         mask.loc,
+                         masks,
+
+                         mask.label = "cell.mask",
+                         mask.ext = "_mask.tif",
+
+                         correct.extent = TRUE,
+                         flip.y = TRUE,
+                         value.modifier = 65535,
+                         array = FALSE
+                         ){
+
+  ### Require
+
+      require('raster')
+      require('hdf5r')
+      require('HDF5Array')
+
+  ### Setup
+
+      message(paste0('Adding masks to ', mask.label))
+
+      spat.names <- names(spatial.dat)
+      spat.names
+
+      mask.names <- gsub(mask.ext, "", masks)
+      mask.names
+
+      mask.check <- (spat.names == mask.names)
+      mask.check
+
+      if(all(mask.check) == FALSE){
+        stop('Error -- list of ROIs does not match the list of masks')
+      }
+
+  ### Read in mask files
+
+      setwd(mask.loc)
+
+      for(i in spat.names){
+        # i <- spat.names[[1]]
+
+        message(paste0("  -- processing ", i))
+
+        if(grepl('.h5', mask.ext)){
+          file.ext <- '.h5'
+        } else {
+          file.ext <- 'other'
+        }
+
+        ## If HDF5 files
+
+            if(file.ext == '.h5'){
+
+              message("     ... reading HDF5 file")
+
+              # h5closeAll()
+              # h5ls(paste0(i, mask.ext))
+
+              mask.img <- h5read(paste0(i, mask.ext), name = 'exported_data')
+              mask.img <- array(as.numeric(mask.img), dim(mask.img))
+              mask.img <- matrix(mask.img, nrow = dim(mask.img)[3], ncol = dim(mask.img)[2])
+              mask.img <- raster(mask.img)
+
+            } else {
+
+        ## If NOT HDF5 files
+
+              if(array == FALSE){
+                mask.img <- readTIFF(paste0(i, mask.ext))
+                mask.img <- raster(mask.img)
+              }
+
+              if(array == TRUE){
+
+                message("     ... reading array")
+
+                mask.img <- raster(paste0(i, mask.ext))
+              }
+
+            }
+
+        ## Correct extent
+
+            if(correct.extent == TRUE){
+              message("     ... correcting extent")
+              extent(mask.img) <- c(0, dim(mask.img)[2], 0,dim(mask.img)[1]) # Y axis - X axis
+            }
+
+        ## Flip Y
+
+            if(flip.y == TRUE){
+              message("     ... flipping Y")
+              mask.img <- flip(mask.img, 'y')
+            }
+
+        ## Finalise
+
+            raster::values(mask.img) <- raster::values(mask.img) * value.modifier
+            names(mask.img) <- mask.label
+            spatial.dat[[i]]$MASKS[[mask.label]]$maskraster <- mask.img
+
+      }
+
+      message("Returning spatial data object with added masks")
+      return(spatial.dat)
+}
+

R/do.add.percell.R

@@ -0,0 +1,29 @@
+#' do.add.percell
+#'
+#' @author Thomas M Ashhurst, \email{thomas.ashhurst@@sydney.edu.au}
+#'
+#' @references \url{https://github.com/ImmuneDynamics/Spectre}.
+#'
+#' @import data.table
+#'
+#' @export
+
+do.add.percell <- function(spatial.dat,
+                           percell.dat,
+                           roi.col,
+                           name = "per.cell"){
+
+  ### Setup
+  message("This is a developmental Spectre-spatial function that is still in testing phase with limited documentation. We recommend only using this function if you know what you are doing.")
+
+  ### Loop
+
+  for(i in names(spatial.dat)){
+    # i <- "20171228_spleen315_500x500_editedforFAS_s1_p9_r2_a2_ac"
+    temp <- percell.dat[percell.dat[[roi.col]] == i,]
+    spatial.dat[[i]]$CPDATA[[name]] <- temp
+  }
+
+  return(spatial.dat)
+
+}

R/do.aggregate.R

@@ -21,6 +21,9 @@
 #'                        plot.title = "Pheatmap",
 #'                        sample.col = "Population",
 #'                        plot.cols = names(exp)[c(2:10)])
+#' @author Thomas M Ashhurst, \email{thomas.ashhurst@@sydney.edu.au}
+#'
+#' @references \url{https://github.com/ImmuneDynamics/Spectre}.
 #'
 #' @import data.table
 #'