Merge pull request #194 from ImmuneDynamics/v1.2.0-beta

Updating v1.1.0 to v1.2.0

.Rbuildignore

@@ -1,2 +1,3 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/check-standard.yaml

@@ -0,0 +1,52 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master, introduce_ci]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          # leave this out for now as it can take too long.
+          # - {os: ubuntu-latest,   r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          dependencies: '"hard"'
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: false
+          args: 'c("--no-examples", "--no-manual", "--no-build-vignettes")'
+          build_args: 'c("--no-manual")'
+          error-on: '"error"'

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 = "[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")
+    person("Thomas", "Ashhurst", , "[email protected]", role = c("aut", "cre")),
+    person("Felix", "Marsh-Wakefield", , "[email protected]", role = "aut"),
+    person("Givanna", "Putri", , "[email protected]", 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()` + file LICENSE
 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
+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)
@@ -14,7 +15,6 @@ export(do.calculate.area)
 export(do.clip)
 export(do.combine.cols)
 export(do.create.outlines)
-export(do.embed.columns)
 export(do.extract)
 export(do.extract.cell.dat)
 export(do.filter)
@@ -30,11 +30,12 @@ export(do.rescale)
 export(do.stats)
 export(do.subsample)
 export(do.zscore)
+export(fast.colour.plot)
+export(fast.multi.plot)
 export(fftRtsne)
 export(make.autograph)
 export(make.colour.plot)
 export(make.multi.plot)
-export(make.network.plot)
 export(make.pheatmap)
 export(make.spatial.plot)
 export(make.volcano.plot)
@@ -45,24 +46,22 @@ export(prep.cytonorm)
 export(read.files)
 export(read.spatial.files)
 export(run.align)
-export(run.chronoclust)
 export(run.cytonorm)
 export(run.fitsne)
 export(run.flowsom)
 export(run.harmony)
 export(run.knn.classifier)
 export(run.pca)
 export(run.phenograph)
-export(run.prepare.chronoclust)
 export(run.rpca)
 export(run.ruv)
 export(run.spatial.analysis)
 export(run.tsne)
 export(run.umap)
+export(spatial)
 export(train.cytonorm)
 export(train.knn.classifier)
 export(write.files)
 export(write.hdf5)
-export(write.sumtables)
 exportClasses(spatial)
 import(data.table)

R/BatchAdjust.R

@@ -1,8 +1,7 @@
-#' BatchAdjust
-#' 
-#' Functions provided for BatchAdjust
-#' 
-#' @export
+# BatchAdjust
+# 
+# Functions provided for BatchAdjust
+# 
 
 ######## Version from https://github.com/i-cyto/CytofBatchAdjust/edit/master/BatchAdjust.R to allow on windows
 

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)
+}