Merge branch 'updates' into introduce_ci

DESCRIPTION

@@ -1,67 +1,80 @@
-Package: Spectre
 Type: Package
-Version: 1.1.0
+Package: Spectre
+Title: High-dimensional cytometry and imaging analysis.
+Version: 1.2.0
 Date: 2023-11-12
-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 = "thomas.ashhurst@sydney.edu.au", role = c("aut", "cre")),
-  person(given = "Felix", family = "Marsh-Wakefield", email = "felix.marsh-wakefield@sydney.edu.au", role = "aut"),
-  person(given = "Givanna", family = "Putri", email = "putri.g@wehi.edu.au", role = "aut")
+    person("Thomas", "Ashhurst", , "thomas.ashhurst@sydney.edu.au", role = c("aut", "cre")),
+    person("Felix", "Marsh-Wakefield", , "felix.marsh-wakefield@sydney.edu.au", role = "aut"),
+    person("Givanna", "Putri", , "putri.g@wehi.edu.au", role = "aut")
   )
+Description: A computational toolkit in R for the integration,
+    exploration, and analysis of high-dimensional single-cell cytometry
+    and imaging data.
+License: `use_mit_license()`
 URL: https://github.com/ImmuneDynamics/Spectre
 BugReports: https://github.com/ImmuneDynamics/Spectre/issues
-Maintainer: Thomas Ashhurst <thomas.ashhurst@sydney.edu.au>
-Depends: R (>= 3.6.0)
-License: MIT Licence
-Encoding: UTF-8
-LazyData: true
-biocViews: flowCore
+Depends: 
+    R (>= 3.6.0)
+biocViews:
 Imports:
+    colorRamps,
+    data.table,
+    dendsort,
+    factoextra,
     flowCore,
-    matrixStats,
-    Biobase,
-    flowViz,
     FlowSOM,
-    rhdf5,
-    HDF5Array,
-    devtools,
-    BiocManager,
-    plyr,
-    dplyr,
-    data.table,
-    tidyr,
-    rstudioapi,
-    Rtsne,
-    umap,
     ggplot2,
+    ggpointdensity,
+    ggpubr,
     ggthemes,
-    scales,
-    colorRamps,
-    RColorBrewer,
     gridExtra,
+    gtools,
+    irlba,
+    parallel,
+    patchwork,
     pheatmap,
-    ggpubr,
-    class,
+    RColorBrewer,
+    rstudioapi,
+    rsvd,
+    Rtsne,
+    scales,
+    scattermore,
+    umap,
+    uwot,
+    viridis
+Suggests:
+    Biobase,
     caret,
+    CytofRUV,
+    CytoNorm,
+    devtools,
+    EnhancedVolcano,
+    exactextractr,
     FNN,
-    ggpointdensity,
-    factoextra,
-    gtools,
-    tidygraph,
-    ggraph,
-    stringr,
-    rsvd,
-    irlba,
-    gridExtra,
+    formatR,
+    harmony,
+    HDF5Array,
+    limma,
+    qs,
     raster,
-    tiff,
-    tidyr,
-    sp,
+    Rcpp,
+    rgdal,
+    rgeos,
+    rhdf5,
+    Rphenograph,
+    s2,
+    Seurat,
+    SeuratObject,
     sf,
+    SingleCellExperiment,
+    sp,
     stars,
-    qs,
-    s2,
-    exactextractr,
-RoxygenNote: 7.2.3
+    testthat (>= 3.0.0),
+    tiff,
+    usethis
+Config/testthat/edition: 3
+Encoding: UTF-8
+LazyData: true
 Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.1

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
-export()
+export(adjust.files)
+export(check.files)
 export(create.dt)
 export(create.stats)
 export(create.sumtable)

R/adjust.files.R

@@ -0,0 +1,27 @@
+#' adjust.files
+#' 
+#' @param dat List of data.tables, typically one per 'sample'
+#' @param colnames.table A data.table of column names. First column contains the current names, second column contains the new names to update to.
+#' 
+#' @export
+
+adjust.files <- function(dat, colnames.table){
+
+  new.names <- colnames.table
+
+  for(a in names(dat)){
+    # a <- names(dat)[1]
+
+    for(i in c(1:nrow(new.names))){
+      # i <- 1
+      old <- new.names[i,1][[1]]
+      new <- new.names[i,2][[1]]
+
+      if(length(which(names(dat[[a]]) == old)) == 1){
+        names(dat[[a]])[which(names(dat[[a]]) == old)] <- new
+      }
+    }
+  }
+
+  return(dat)
+}

R/check.files.R

@@ -0,0 +1,77 @@
+#' check.files
+#' 
+#' @param dat List of data.tables, typically one per 'sample'
+#' 
+#' @export
+
+check.files <- function(dat){
+
+  ###
+
+  files <- names(dat)
+
+  file.table <- data.table('FileName' = files)
+  setorderv(file.table, "FileName")
+  file.table
+
+  colcheck.list <- list()
+  colname.list <- list()
+
+  ###
+
+  for(i in files){
+    colcheck.list[[i]] <- dat[[i]][1,]
+    colname.list[[i]] <- names(dat[[i]])
+  }
+
+  colcheck.list
+  colname.list
+
+  ### Condensing column check data
+
+  colcheck.dat <- rbindlist(colcheck.list, fill = TRUE)
+  colcheck.dat <- as.data.table(!is.na(colcheck.dat))
+  colcheck.dat
+
+  ### Condensing column names summary
+
+  all.colnames <- unique(unlist(colname.list))
+  all.colnames
+
+  colnames.summary <- list()
+
+  for(a in all.colnames){
+    # a <- all.colnames[1]
+    colnames.summary[[a]] <- length(which(colcheck.dat[[a]]))
+  }
+
+  colnames.summary <- rbindlist(list(colnames.summary))
+  colnames.summary
+
+  ###
+
+  colcheck.dat$FileName <- files
+  colcheck.dat
+
+  ### Making colname table
+
+  colname.table <- data.table('Column name' = all.colnames, 'New name' = all.colnames)
+  colname.table
+
+  ### Condensing test data
+
+  tempdat <- rbindlist(dat, fill = TRUE)
+  tempdat
+
+  ### Output
+
+  res <- list('Column check' = colcheck.dat,
+              'Column summary' = colnames.summary,
+              'All column names' = all.colnames,
+              'Column name table' = colname.table,
+              'Test data' = tempdat)
+
+  ### Return
+
+  return(res)
+}