Merge pull request #1 from lthealy/master

Paper submission related updates
rmoffitt · Nov 30, 2022 · 3c0207f · 3c0207f
2 parents 3a3f568 + 1a27f93
commit 3c0207f
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -8,13 +8,13 @@ Description: Downloads and prepares public PDAC data for analysis, and provides
 License: MIT
 Encoding: UTF-8
 LazyData: TRUE
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.1
 Suggests: testthat,
           decoderr
 biocViews:
 Imports: Biobase,bioDist,BiocManager,
          ConsensusClusterPlus,
-         decoderr,
+         DESeq2,
          foreign,
          GEOquery,
          ggplot2,
@@ -37,6 +37,7 @@ Imports: Biobase,bioDist,BiocManager,
          scales,
          shiny,
          shinyjs,
+         shinythemes,
          SingleCellExperiment,
          stringi,
          stringr,

diff --git a/NAMESPACE b/NAMESPACE
@@ -13,6 +13,7 @@ export(generate_mouse_data_set_list)
 export(getSideColors)
 export(heatmap.3)
 export(implement_PAMG)
+export(install_dependencies)
 export(other_cluster_based_subtyping)
 export(parse_ICGC)
 export(parse_Moffitt_supplement)

diff --git a/R/generate_data_set_list.R b/R/generate_data_set_list.R
@@ -31,8 +31,8 @@ generate_data_set_list <- function() {
                      "Seino_GEO_array",
                      "TCGA_PAAD"))
 
-  save(list = c("data_set_list"),
-       file = "./data/data_set_list.RData")
+  saveRDS(data_set_list,
+          file = "./data/data_set_list.rds")
 
   # for(i in data_set_list$variablenames){
   #   writeLines('----------------------------')

diff --git a/R/generate_mouse_data_set_list.R b/R/generate_mouse_data_set_list.R
@@ -3,11 +3,11 @@
 #' @export
 
 generate_mouse_data_set_list <- function() {
-   mouse_data_set_list <- data.frame(labels=c(
-      "Moffitt seq, 2015"),
-      variablenames =c("Moffitt_S2.Mm"))
+  mouse_data_set_list <- data.frame(labels=c(
+    "Moffitt seq, 2015"),
+    variablenames =c("Moffitt_S2.Mm"))
 
-   save(list = c("mouse_data_set_list"),
-        file = "./data/mouse_data_set_list.RData")
-   return(NULL)
+  saveRDS(mouse_data_set_list,
+          file = "./data/mouse_data_set_list.rds")
+  return(NULL)
 }
diff --git a/R/install.dependencies.R b/R/install.dependencies.R
@@ -1,183 +1,148 @@
-# message("Ensuring appropriate install of all dependencies from both CRAN and BioConductor")
-# if (!require("plyr")) {
-#   install.packages("plyr",repos="http://cran.rstudio.com/")
-# }
-# if (!require("tidyverse")) {
-#   install.packages("tidyverse",repos="http://cran.rstudio.com/")
-# }
-# if (!require("devtools")) {
-#   install.packages("devtools",repos="http://cran.rstudio.com/")
-# }
-#
-# if (!require("testthat")) {
-#   install.packages("testthat",repos="http://cran.rstudio.com/")
-# }
-# if (!require("reshape2")) {
-#   install.packages("reshape2",repos="http://cran.rstudio.com/")
-# }
-# if (!require("gplots")) {
-#   install.packages("gplots",repos="http://cran.rstudio.com/")
-# }
-# if (!require("RColorBrewer")) {
-#   install.packages("RColorBrewer",repos="http://cran.rstudio.com/")
-# }
-# if (!require("shiny")) {
-#   install.packages("shiny",repos="http://cran.rstudio.com/")
-# }
-# if (!require("scales")) {
-#   install.packages("scales",repos="http://cran.rstudio.com/")
-# }
-# if (!require("ggplot2")) {
-#   install.packages("ggplot2",repos="http://cran.rstudio.com/")
-# }
-# if (!require("openxlsx")) {
-#   install.packages("openxlsx",repos="http://cran.rstudio.com/")
-# }
-# if (!require("Rtsne")) {
-#   install.packages("Rtsne",repos="http://cran.rstudio.com/")
-# }
-# if (!require("GGally")) {
-#   install.packages("GGally",repos="http://cran.rstudio.com/")
-# }
-# if (!require("ggpubr")) {
-#   install.packages("ggpubr",repos="http://cran.rstudio.com/")
-# }
-# if (!require("ggrepel")) {
-#   install.packages("ggrepel",repos="http://cran.rstudio.com/")
-# }
-# if (!require("pROC")) {
-#   install.packages("pROC",repos="http://cran.rstudio.com/")
-# }
-# if (!require("survminer")) {
-#   install.packages("survminer",repos="http://cran.rstudio.com/")
-# }
-# if (!require("nlme")) {
-#   install.packages("nlme",repos="http://cran.rstudio.com/")
-# }
-# if (!require("foreign")) {
-#   install.packages("foreign",repos="http://cran.rstudio.com/")
-# }
-# if (!require("shinyjs")) {
-#   install.packages("shinyjs",repos="http://cran.rstudio.com/")
-# }
-# if (!require("decoderr")) {
-#   devtools::install_github("laurapeng/decoderr")
-# }
-# if (!require("rlang")) {
-#   install.packages("rlang",repos="http://cran.rstudio.com/")
-# }
-# if (!require("stringi")) {
-#   install.packages("stringi",repos="http://cran.rstudio.com/")
-# }
-# if (!require("shinythemes")) {
-#   install.packages("shinythemes",repos="http://cran.rstudio.com/")
-# }
-# if (!require("pdacmolgrad")) {
-#   devtools::install_github("RemyNicolle/pdacmolgrad")
-# }
-# if (!require("Seurat")) {
-#   install.packages("Seurat")
-# }
-# if (!require("mosaic")) {
-#   install.packages("mosaic")
-# }
-# if (!require("Cairo")) {
-#   install.packages("Cairo")
-# }
-#
-# myversion <- as.numeric(R.Version()$major)+0.1*as.numeric(R.Version()$minor)
-# if( myversion < 3.5){
-#   source("https://bioconductor.org/biocLite.R")
-#   biocLite()
-#
-#   if (!require("Biobase")) {
-#     biocLite("Biobase")
-#   }
-#
-#   if (!require("AnnotationDbi")) {
-#     biocLite("AnnotationDbi")
-#   }
-#
-#   if (!require("org.Hs.eg.db")) {
-#     biocLite("org.Hs.eg.db")
-#   }
-#   if (!require("illuminaHumanv4.db")) {
-#     biocLite("illuminaHumanv4.db")
-#   }
-#
-#   if (!require("ConsensusClusterPlus")) {
-#     biocLite("ConsensusClusterPlus")
-#   }
-#   if (!require("GEOquery")) {
-#     biocLite("GEOquery")
-#   }
-#   if (!require("bioDist")) {
-#     biocLite("bioDist")
-#   }
-#   if (!require("preprocessCore")) {
-#     biocLite("preprocessCore")
-#   }
-#   if (!require("sva")) {
-#     biocLite("sva")
-#   }
-#   if (!require("limma")) {
-#     biocLite("limma")
-#   }
-# } else {
-#   if (!require("BiocManager")) {
-#     install.packages("BiocManager",repos="http://cran.rstudio.com/")
-#   }
-#
-#   if (!require("Biobase")) {
-#     BiocManager::install("Biobase")
-#   }
-#
-#   if (!require("AnnotationDbi")) {
-#     BiocManager::install("AnnotationDbi")
-#   }
-#
-#   if (!require("org.Hs.eg.db")) {
-#     BiocManager::install("org.Hs.eg.db")
-#   }
-#   if (!require("illuminaHumanv4.db")) {
-#     BiocManager::install("illuminaHumanv4.db")
-#   }
-#
-#   if (!require("ConsensusClusterPlus")) {
-#     BiocManager::install("ConsensusClusterPlus")
-#   }
-#   if (!require("GEOquery")) {
-#     BiocManager::install("GEOquery")
-#   }
-#   if (!require("bioDist")) {
-#     BiocManager::install("bioDist")
-#   }
-#   if (!require("preprocessCore")) {
-#     BiocManager::install("preprocessCore")
-#   }
-#   if (!require("sva")) {
-#     BiocManager::install("sva")
-#   }
-#   if (!require("yaml")) {
-#     BiocManager::install("yaml")
-#   }
-#   if (!require("hgu219.db")) {
-#     BiocManager::install("hgu219.db")
-#   }
-#   if (!require("oligo")) {
-#     BiocManager::install("oligo")
-#   }
-#   if (!require("SingleCellExperiment")) {
-#     BiocManager::install("SingleCellExperiment")
-#   }
-#   if (!require("ggpubr")) {
-#     BiocManager::install("ggpubr")
-#   }
-#   if (!require("DESeq2")) {
-#     BiocManager::install("DESeq2")
-#   }
-#   if (!require("limma")) {
-#     BiocManager::install("limma")
-#   }
-# }
-# message("pdacR dependency install complete")
+#' @export
+
+install_dependencies <- function(){
+  message("Ensuring appropriate install of all dependencies from both CRAN and BioConductor")
+  if (!require("plyr")) {
+    install.packages("plyr",repos="http://cran.rstudio.com/")
+  }
+  if (!require("tidyverse")) {
+    install.packages("tidyverse",repos="http://cran.rstudio.com/")
+  }
+  if (!require("devtools")) {
+    install.packages("devtools",repos="http://cran.rstudio.com/")
+  }
+
+  if (!require("testthat")) {
+    install.packages("testthat",repos="http://cran.rstudio.com/")
+  }
+  if (!require("reshape2")) {
+    install.packages("reshape2",repos="http://cran.rstudio.com/")
+  }
+  if (!require("gplots")) {
+    install.packages("gplots",repos="http://cran.rstudio.com/")
+  }
+  if (!require("RColorBrewer")) {
+    install.packages("RColorBrewer",repos="http://cran.rstudio.com/")
+  }
+  if (!require("shiny")) {
+    install.packages("shiny",repos="http://cran.rstudio.com/")
+  }
+  if (!require("scales")) {
+    install.packages("scales",repos="http://cran.rstudio.com/")
+  }
+  if (!require("ggplot2")) {
+    install.packages("ggplot2",repos="http://cran.rstudio.com/")
+  }
+  if (!require("openxlsx")) {
+    install.packages("openxlsx",repos="http://cran.rstudio.com/")
+  }
+  if (!require("Rtsne")) {
+    install.packages("Rtsne",repos="http://cran.rstudio.com/")
+  }
+  if (!require("GGally")) {
+    install.packages("GGally",repos="http://cran.rstudio.com/")
+  }
+  if (!require("ggpubr")) {
+    install.packages("ggpubr",repos="http://cran.rstudio.com/")
+  }
+  if (!require("ggrepel")) {
+    install.packages("ggrepel",repos="http://cran.rstudio.com/")
+  }
+  if (!require("pROC")) {
+    install.packages("pROC",repos="http://cran.rstudio.com/")
+  }
+  if (!require("survminer")) {
+    install.packages("survminer",repos="http://cran.rstudio.com/")
+  }
+  if (!require("nlme")) {
+    install.packages("nlme",repos="http://cran.rstudio.com/")
+  }
+  if (!require("foreign")) {
+    install.packages("foreign",repos="http://cran.rstudio.com/")
+  }
+  if (!require("shinyjs")) {
+    install.packages("shinyjs",repos="http://cran.rstudio.com/")
+  }
+  # if (!require("decoderr")) {
+  #   devtools::install_github("laurapeng/decoderr")
+  # }
+  if (!require("rlang")) {
+    install.packages("rlang",repos="http://cran.rstudio.com/")
+  }
+  if (!require("stringi")) {
+    install.packages("stringi",repos="http://cran.rstudio.com/")
+  }
+  if (!require("shinythemes")) {
+    install.packages("shinythemes",repos="http://cran.rstudio.com/")
+  }
+  if (!require("pdacmolgrad")) {
+    devtools::install_github("RemyNicolle/pdacmolgrad")
+  }
+  if (!require("Seurat")) {
+    install.packages("Seurat")
+  }
+  if (!require("mosaic")) {
+    install.packages("mosaic")
+  }
+  if (!require("Cairo")) {
+    install.packages("Cairo")
+  }
+
+  if (!require("BiocManager")) {
+    install.packages("BiocManager",repos="http://cran.rstudio.com/")
+  }
+
+  if (!require("Biobase")) {
+    BiocManager::install("Biobase")
+  }
+
+  if (!require("AnnotationDbi")) {
+    BiocManager::install("AnnotationDbi")
+  }
+
+  if (!require("org.Hs.eg.db")) {
+    BiocManager::install("org.Hs.eg.db")
+  }
+  if (!require("illuminaHumanv4.db")) {
+    BiocManager::install("illuminaHumanv4.db")
+  }
+
+  if (!require("ConsensusClusterPlus")) {
+    BiocManager::install("ConsensusClusterPlus")
+  }
+  if (!require("GEOquery")) {
+    BiocManager::install("GEOquery")
+  }
+  if (!require("bioDist")) {
+    BiocManager::install("bioDist")
+  }
+  if (!require("preprocessCore")) {
+    BiocManager::install("preprocessCore")
+  }
+  if (!require("sva")) {
+    BiocManager::install("sva")
+  }
+  if (!require("yaml")) {
+    BiocManager::install("yaml")
+  }
+  if (!require("hgu219.db")) {
+    BiocManager::install("hgu219.db")
+  }
+  if (!require("oligo")) {
+    BiocManager::install("oligo")
+  }
+  if (!require("SingleCellExperiment")) {
+    BiocManager::install("SingleCellExperiment")
+  }
+  if (!require("ggpubr")) {
+    BiocManager::install("ggpubr")
+  }
+  if (!require("DESeq2")) {
+    BiocManager::install("DESeq2")
+  }
+  if (!require("limma")) {
+    BiocManager::install("limma")
+  }
+
+  message("pdacR dependency install complete")
+}