Development/Dependencies.R

In vertesy/Seurat.utils: Seurat.utils - utility functions for Seurat

Dependency file generated on Fri Mar 22 15:39:38 2024 

#################################################################################################### 
Seurat.utils.less.used.R
#################################################################################################### 
$`c("package:Seurat.utils", "package:CodeAndRoll2")`
[1] "grepv"

$`c("package:Seurat.utils", "package:ggplot2")`
[1] "element_text" "ggtitle"      "theme"       

$`c("package:Seurat.utils", "package:Seurat", "package:SeuratObject")`
[1] "CreateSeuratObject" "FetchData"         

$`c("package:Seurat.utils", "package:Seurat")`
[1] "DimPlot"  "NoLegend" "Read10X" 

$`c("package:Seurat.utils", "package:Stringendo")`
[1] "iprint"

$`c("package:sp", "package:base")`
[1] "split"

$`c("package:sp", "package:graphics", "package:base")`
[1] "plot"

$`package:base`
 [1] ".Deprecated"  "all"          "any"          "as.character" "as.matrix"    "basename"     "c"           
 [8] "colnames"     "data.frame"   "do.call"      "file.exists"  "file.path"    "grep"         "grepl"       
[15] "gsub"         "ifelse"       "is.list"      "is.null"      "length"       "list"         "list.dirs"   
[22] "list.files"   "match"        "message"      "names"        "paste0"       "print"        "range"       
[29] "return"       "rownames"     "saveRDS"      "sort"         "sprintf"      "stop"         "toupper"     
[36] "warning"     

$`package:CodeAndRoll2`
[1] "list.fromNames" "translate"      "unlapply"      

$`package:graphics`
[1] "points"

$`package:Seurat.utils`
[1] "plot_grid"         "principal_curve"   "save_plot"         "SoupChannel"       "UpdateGenesSeurat"
[6] "whiskers"          "wplot_save_this"  

$`package:Stringendo`
[1] "kpp" "ppp" "ppu"

$`package:utils`
[1] "read.csv"

c("Seurat.utils", "CodeAndRoll2")
c("Seurat.utils", "ggplot2")
c("Seurat.utils", "Seurat", "SeuratObject")
c("Seurat.utils", "Seurat")
c("Seurat.utils", "Stringendo")
c("sp", "base")
c("sp", "graphics", "base")
base
CodeAndRoll2
graphics
Seurat.utils
Stringendo
utils
#################################################################################################### 
Seurat.Utils.Metadata.R
#################################################################################################### 
$`c("package:Seurat.utils", "package:CodeAndRoll2")`
[1] "as.named.vector.df" "grepv"             

$`c("package:Seurat.utils", "package:ggExpress")`
[1] "qbarplot" "qqSave"  

$`c("package:Seurat.utils", "package:ggpubr")`
[1] "group_by"

$`c("package:Seurat.utils", "package:Seurat", "package:SeuratObject")`
[1] "AddMetaData"  "GetAssayData" "Idents"      

$`c("package:Seurat.utils", "package:Seurat")`
[1] "FindTransferAnchors" "TransferData"       

$`c("package:Seurat.utils", "package:SeuratObject", "package:base")`
[1] "colSums"

$`c("package:Seurat.utils", "package:stats")`
[1] "cor"    "filter"

$`c("package:Seurat.utils", "package:Stringendo")`
[1] "iprint"               "kollapse"             "percentage_formatter"

$`c("package:SeuratObject", "package:base")`
[1] "intersect"

$`character(0)`
 [1] "across"            "all_of"            "as.numeric.wNames" "desc"              "group_by_at"      
 [6] "imessage"          "mixedsort"         "n"                 "nr.unique"         "write.simple.tsv" 

$`package:base`
 [1] "all"           "any"           "as.character"  "as.data.frame" "basename"      "c"            
 [7] "cat"           "cbind"         "ceiling"       "character"     "colnames"      "dim"          
[13] "do.call"       "dput"          "duplicated"    "file.exists"   "floor"         "grep"         
[19] "gsub"          "ifelse"        "inherits"      "invisible"     "is.character"  "is.data.frame"
[25] "is.list"       "is.logical"    "is.na"         "is.nan"        "is.null"       "is.vector"    
[31] "isFALSE"       "lapply"        "length"        "levels"        "list"          "make.names"   
[37] "make.unique"   "match"         "max"           "message"       "min"           "names"        
[43] "ncol"          "nrow"          "paste"         "paste0"        "print"         "rep"          
[49] "return"        "round"         "rownames"      "sample"        "sapply"        "scale"        
[55] "seq_along"     "setdiff"       "sprintf"       "stopifnot"     "sub"           "substitute"   
[61] "sum"           "table"         "unique"        "warning"       "which"        

$`package:CodeAndRoll2`
[1] "colMax"        "intersect.ls"  "trail"         "translate"     "unlapply"      "vec.fromNames"
[7] "which_names"  

$`package:ggExpress`
[1] "qpie"

$`package:ggplot2`
[1] "position_stack" "sym"            "vars"          

$`package:ggpubr`
[1] "ggbarplot"

$`package:MarkdownHelpers`
[1] "stopif"

$`package:methods`
[1] "is"        "slotNames"

$`package:Seurat.utils`
 [1] ".replace_by_most_frequent_categories" "arrange"                             
 [3] "check.genes"                          "clUMAP"                              
 [5] "deframe"                              "FirstCol2RowNames"                   
 [7] "GetClusteringRuns"                    "GetNamedClusteringRuns"              
 [9] "GetOrderedClusteringRuns"             "ggcorrplot"                          
[11] "melt"                                 "pheatmap"                            
[13] "qUMAP"                                "read_rds"                            
[15] "summarise"                            "summarize_all"                       
[17] "summarize_at"                         "wplot_save_pheatmap"                 
[19] "xsave"                               

$`package:stats`
[1] "median"   "setNames"

$`package:Stringendo`
[1] "FixPlotName" "kpp"         "kpps"        "ppp"         "sppp"       

$`package:utils`
[1] "head" "tail"

c("Seurat.utils", "CodeAndRoll2")
c("Seurat.utils", "ggExpress")
c("Seurat.utils", "ggpubr")
c("Seurat.utils", "Seurat", "SeuratObject")
c("Seurat.utils", "Seurat")
c("Seurat.utils", "SeuratObject", "base")
c("Seurat.utils", "stats")
c("Seurat.utils", "Stringendo")
c("SeuratObject", "base")
character(0)
base
CodeAndRoll2
ggExpress
ggplot2
ggpubr
MarkdownHelpers
methods
Seurat.utils
stats
Stringendo
utils
#################################################################################################### 
Seurat.Utils.R
#################################################################################################### 
$.GlobalEnv
[1] "list.dirs.depth.n"      "memory.biggest.objects" "say"                   

$`c("package:Seurat.utils", "package:base")`
[1] "crossprod"  "tcrossprod"

$`c("package:Seurat.utils", "package:CodeAndRoll2")`
[1] "as.named.vector.df" "grepv"             

$`c("package:Seurat.utils", "package:DatabaseLinke.R")`
[1] "qHGNC"

$`c("package:Seurat.utils", "package:ggExpress")`
[1] "qbarplot"   "qhistogram" "qqSave"     "qscatter"   "qvenn"     

$`c("package:Seurat.utils", "package:ggplot2")`
[1] "geom_hline" "geom_point" "geom_vline" "ggplot"     "ggsave"     "ggtitle"    "theme"     

$`c("package:Seurat.utils", "package:ggpubr")`
[1] "group_by"

$`c("package:Seurat.utils", "package:MarkdownHelpers")`
[1] "llogit"              "llprint"             "ww.assign_to_global"

$`c("package:Seurat.utils", "package:PackageTools")`
[1] "isAvailable"

$`c("package:Seurat.utils", "package:Seurat", "package:SeuratObject")`
[1] "AddMetaData"        "CreateSeuratObject" "GetAssayData"       "Idents"             "RenameCells"       
[6] "VariableFeatures"   "WhichCells"        

$`c("package:Seurat.utils", "package:Seurat")`
[1] "FindClusters"         "FindNeighbors"        "FindVariableFeatures" "Read10X"             
[5] "RunPCA"               "RunTSNE"              "RunUMAP"              "ScaleData"           

$`c("package:Seurat.utils", "package:SeuratObject", "package:base")`
[1] "colMeans" "colSums"  "rowSums" 

$`c("package:Seurat.utils", "package:stats")`
[1] "cor"    "filter"

$`c("package:Seurat.utils", "package:Stringendo")`
[1] "iprint"               "kollapse"             "percentage_formatter"

$`c("package:SeuratObject", "package:base")`
[1] "intersect"

$`character(0)`
 [1] "barplot_label"     "count"             "desc"              "distinct"          "enframe"          
 [6] "getProject"        "group_by_at"       "kppc"              "kppws"             "lst"              
[11] "mixedsort"         "n"                 "percent_rank"      "printProgress"     "RemoveWhitespaces"
[16] "select_at"         "spread"            "str_extract"       "unnest"            "write.simple.tsv" 

$`package:base`
  [1] ".Deprecated"      "all"              "any"              "apply"            "as.character"    
  [6] "as.data.frame"    "as.environment"   "as.list"          "as.matrix"        "as.name"         
 [11] "as.numeric"       "assign"           "basename"         "browser"          "c"               
 [16] "cat"              "cbind"            "character"        "class"            "colnames"        
 [21] "data.frame"       "deparse"          "diag"             "dim"              "dir.create"      
 [26] "dir.exists"       "dirname"          "dput"             "droplevels"       "exists"          
 [31] "file.copy"        "file.exists"      "file.path"        "file.remove"      "floor"           
 [36] "format"           "gc"               "getwd"            "grep"             "grepl"           
 [41] "gsub"             "identical"        "ifelse"           "inherits"         "invisible"       
 [46] "is.character"     "is.list"          "is.logical"       "is.null"          "is.numeric"      
 [51] "isFALSE"          "lapply"           "length"           "library"          "list"            
 [56] "list.dirs"        "list.files"       "log10"            "log2"             "make.names"      
 [61] "make.unique"      "match"            "max"              "mean"             "message"         
 [66] "min"              "names"            "nchar"            "ncol"             "nrow"            
 [71] "options"          "paste"            "paste0"           "print"            "rbind"           
 [76] "readline"         "readRDS"          "rep"              "require"          "return"          
 [81] "round"            "rownames"         "sample"           "sapply"           "save.image"      
 [86] "saveRDS"          "scale"            "seq_along"        "set.seed"         "setdiff"         
 [91] "signif"           "sort"             "sprintf"          "sqrt"             "stop"            
 [96] "stopifnot"        "subset"           "substitute"       "substr"           "sum"             
[101] "suppressWarnings" "Sys.info"         "Sys.setenv"       "Sys.time"         "system"          
[106] "t"                "table"            "toupper"          "trimws"           "try"             
[111] "union"            "unique"           "unlist"           "warning"          "which"           

$`package:CodeAndRoll2`
 [1] "any.duplicated"    "col2named.vec.tbl" "idim"              "iround"            "list.fromNames"   
 [6] "matrix.fromNames"  "pc_TRUE"           "rowMax"            "rowMin"            "sem"              
[11] "sort.decreasing"   "sortbyitsnames"    "splitbyitsnames"   "symdiff"           "trail"            
[16] "translate"         "unlapply"          "which_names"      

$`package:ggExpress`
[1] "qpie"

$`package:ggplot2`
[1] "aes"                "geom_abline"        "scale_alpha_manual" "sym"                "xlab"              
[6] "ylab"              

$`package:MarkdownHelpers`
[1] "filter_HP" "filter_LP" "stopif"    "wcolorize"

$`package:methods`
[1] "is"   "slot"

$`package:Seurat.utils`
 [1] ".check_and_rename"                     ".checkListElements"                   
 [3] ".getCPUsCBE"                           ".getNrPCs"                            
 [5] ".getNrScaledFeatures"                  ".saveRDS.compress.in.BG"              
 [7] "addMetaDataSafe"                       "arrange"                              
 [9] "as_tibble"                             "BackupReduction"                      
[11] "calc.q99.Expression.and.set.all.genes" "check.genes"                          
[13] "checkGeneSymbols"                      "clUMAP"                               
[15] "create_set_OutDir"                     "deframe"                              
[17] "dir_ls"                                "downsampleSeuObj"                     
[19] "dropLevelsSeurat"                      "FirstCol2RowNames"                    
[21] "foreach"                               "geom_text_repel"                      
[23] "GetClusteringRuns"                     "getDoParRegistered"                   
[25] "GetNamedClusteringRuns"                "GetTopMarkersDF"                      
[27] "GetUpdateStats"                        "gunzip"                               
[29] "gzip"                                  "HGNC.EnforceUnique"                   
[31] "IntersectGeneLsWithObject"             "isave.RDS"                            
[33] "jJaccardIndexBinary"                   "jJaccardIndexVec"                     
[35] "job"                                   "multi_clUMAP.A4"                      
[37] "multiFeaturePlot.A4"                   "pheatmap"                             
[39] "plotQUMAPsInAFolder"                   "qClusteringUMAPS"                     
[41] "qMarkerCheck.BrainOrg"                 "qQC.plots.BrainOrg"                   
[43] "qread"                                 "qsave"                                
[45] "qUMAP"                                 "read_tsv"                             
[47] "read.simple.tsv"                       "removeResidualSmallClusters"          
[49] "RenameGenesSeurat"                     "rownames_to_column"                   
[51] "rowQuantiles"                          "rowSums2"                             
[53] "sampleNpc"                             "scPlotPCAvarExplained"                
[55] "select"                                "SetupReductionsNtoKdimensions"        
[57] "slice"                                 "SmallestNonAboveX"                    
[59] "sparse.cor"                            "str_split_fixed"                      
[61] "summarize"                             "suPlotVariableFeatures"               
[63] "tic"                                   "toc"                                  
[65] "top_n"                                 "UpdateGenesSeurat"                    
[67] "vroom"                                 "wbarplot"                             
[69] "whist"                                 "wlegend"                              
[71] "wplot"                                 "wplot_save_pheatmap"                  
[73] "ww.get.1st.Seur.element"               "xsave"                                

$`package:SeuratObject`
[1] "LayerData" "Layers"    "plan"     

$`package:stats`
[1] "ecdf"     "median"   "quantile"

$`package:Stringendo`
 [1] "FixPath"                  "flag.nameiftrue"          "idate"                   
 [4] "kpp"                      "kppd"                     "kpps"                    
 [7] "kppu"                     "ParseFullFilePath"        "ppp"                     
[10] "ReplaceRepeatedSlashes"   "ReplaceSpecialCharacters" "sppp"                    

$`package:utils`
[1] "head" "str" 

.GlobalEnv
c("Seurat.utils", "base")
c("Seurat.utils", "CodeAndRoll2")
c("Seurat.utils", "DatabaseLinke.R")
c("Seurat.utils", "ggExpress")
c("Seurat.utils", "ggplot2")
c("Seurat.utils", "ggpubr")
c("Seurat.utils", "MarkdownHelpers")
c("Seurat.utils", "PackageTools")
c("Seurat.utils", "Seurat", "SeuratObject")
c("Seurat.utils", "Seurat")
c("Seurat.utils", "SeuratObject", "base")
c("Seurat.utils", "stats")
c("Seurat.utils", "Stringendo")
c("SeuratObject", "base")
character(0)
base
CodeAndRoll2
ggExpress
ggplot2
MarkdownHelpers
methods
Seurat.utils
SeuratObject
stats
Stringendo
utils
#################################################################################################### 
Seurat.Utils.Visualization.R
#################################################################################################### 
$.GlobalEnv
[1] "oo"

$`c("package:Seurat.utils", "package:CodeAndRoll2")`
[1] "as_tibble_from_namedVec"     "as.named.vector.df"          "clip.outliers.at.percentile"

$`c("package:Seurat.utils", "package:ggExpress")`
[1] "qA4_grid_plot" "qbarplot"      "qbarplot.df"   "qhistogram"    "qqSave"       

$`c("package:Seurat.utils", "package:ggplot2")`
 [1] "coord_fixed"       "element_text"      "geom_bar"          "geom_hline"        "geom_point"       
 [6] "geom_text"         "geom_vline"        "ggplot"            "ggsave"            "ggtitle"          
[11] "labs"              "scale_fill_manual" "scale_x_log10"     "scale_y_log10"     "theme"            
[16] "theme_classic"     "theme_linedraw"   

$`c("package:Seurat.utils", "package:ggpubr")`
[1] "group_by"

$`c("package:Seurat.utils", "package:graphics")`
[1] "layout" "par"    "text"  

$`c("package:Seurat.utils", "package:MarkdownHelpers")`
[1] "color_check" "llprint"    

$`c("package:Seurat.utils", "package:Seurat", "package:SeuratObject")`
[1] "DefaultAssay"     "Embeddings"       "FetchData"        "GetAssayData"     "VariableFeatures"

$`c("package:Seurat.utils", "package:Seurat")`
 [1] "DimPlot"             "DiscretePalette"     "FeaturePlot"         "FeatureScatter"     
 [5] "LabelPoints"         "NoAxes"              "NoLegend"            "RunPCA"             
 [9] "RunTSNE"             "RunUMAP"             "SplitObject"         "VariableFeaturePlot"
[13] "VlnPlot"            

$`c("package:Seurat.utils", "package:SeuratObject", "package:base")`
[1] "colSums" "rowSums"

$`c("package:Seurat.utils", "package:stats")`
[1] "cor"      "cor.test"

$`c("package:Seurat.utils", "package:Stringendo")`
[1] "iprint"               "kollapse"             "percentage_formatter"

$`c("package:SeuratObject", "package:base")`
[1] "intersect"

$`c("package:sp", "package:base")`
[1] "split"

$`character(0)`
 [1] "barplot_label"              "create_set_Original_OutDir" "FeatureHeatmap"            
 [4] "FirstCol2RowNames.as.df"    "imessage"                   "kppc"                      
 [7] "kppws"                      "left_join"                  "n"                         
[10] "na.replace"                 "nr.unique"                  "percent"                   
[13] "sppu"                       "str_extract"                "ungroup"                   

$`package:base`
 [1] ".Deprecated"    "abs"            "all"            "anyNA"          "apply"          "as.character"  
 [7] "as.environment" "as.factor"      "as.name"        "as.numeric"     "assign"         "c"             
[13] "cat"            "cbind"          "ceiling"        "class"          "colnames"       "cut"           
[19] "data.frame"     "deparse"        "do.call"        "environment"    "exists"         "file.exists"   
[25] "file.path"      "floor"          "format"         "getwd"          "gsub"           "ifelse"        
[31] "inherits"       "invisible"      "is.character"   "is.environment" "is.function"    "is.list"       
[37] "is.logical"     "is.na"          "is.null"        "is.numeric"     "isFALSE"        "isTRUE"        
[43] "lapply"         "length"         "levels"         "list"           "list2env"       "make.names"    
[49] "max"            "mean"           "message"        "min"            "missing"        "names"         
[55] "ncol"           "nrow"           "nzchar"         "on.exit"        "paste"          "paste0"        
[61] "print"          "return"         "rev"            "rm"             "round"          "row.names"     
[67] "rownames"       "sample"         "sapply"         "seq"            "seq_along"      "set.seed"      
[73] "setdiff"        "setwd"          "sort"           "sprintf"        "stop"           "stopifnot"     
[79] "substitute"     "sum"            "table"          "tapply"         "toupper"        "try"           
[85] "unique"         "unlist"         "warning"       

$`package:CodeAndRoll2`
 [1] "clip.at.fixed.value"    "cv"                     "iround"                 "na.omit.strip"         
 [5] "pc_TRUE"                "rowDivide"              "split_vec_to_list_by_N" "splitbyitsnames"       
 [9] "translate"              "unlapply"              

$`package:ggplot2`
 [1] "aes"                 "annotation_logticks" "element_blank"       "element_rect"       
 [5] "expansion"           "geom_histogram"      "position_fill"       "scale_y_continuous" 
 [9] "scale_y_discrete"    "sym"                 "theme_bw"            "theme_set"          

$`package:ggpubr`
[1] "ggbarplot" "mutate"   

$`package:graphics`
[1] "strwidth"

$`package:grDevices`
[1] "colorRampPalette" "hcl"             

$`package:MarkdownHelpers`
[1] "filter_HP"     "jjpegA4"       "stopif"        "TRUE.unless"   "try.dev.off"   "ww.FnP_parser"

$`package:methods`
[1] "is"

$`package:Seurat.utils`
 [1] ".adjustLayout"                              ".getNrScaledFeatures"                      
 [3] ".parseBasicObjStats"                        ".parseKeyParams"                           
 [5] "Annotate4Plotly3D"                          "BackupReduction"                           
 [7] "brewer.pal"                                 "check.genes"                               
 [9] "clUMAP"                                     "create_set_OutDir"                         
[11] "create_set_SubDir"                          "deframe"                                   
[13] "DiscretePaletteSafe"                        "FirstCol2RowNames"                         
[15] "getCellIDs.from.meta"                       "GetClusteringRuns"                         
[17] "getDiscretePaletteObj"                      "GetNamedClusteringRuns"                    
[19] "GetOrderedClusteringRuns"                   "GetTopMarkers"                             
[21] "gg_color_hue"                               "ggdraw"                                    
[23] "ggsave2"                                    "group_by_"                                 
[25] "hue_pal"                                    "multiFeaturePlot.A4"                       
[27] "percent_format"                             "pheatmap"                                  
[29] "plot_grid"                                  "plot_ly"                                   
[31] "plot3D.umap"                                "plot3D.umap.gene"                          
[33] "qUMAP"                                      "RecallReduction"                           
[35] "rich.colors"                                "sample_n"                                  
[37] "save_plot"                                  "SavePlotlyAsHtml"                          
[39] "saveWidget"                                 "scCalcPCAVarExplained"                     
[41] "select"                                     "shorten_clustering_names"                  
[43] "summarise"                                  "summarize"                                 
[45] "tic"                                        "toc"                                       
[47] "toTitleCase"                                "wbarplot"                                  
[49] "wplot_save_pheatmap"                        "ww.check.if.3D.reduction.exist"            
[51] "ww.check.quantile.cutoff.and.clip.outliers"

$`package:stats`
[1] "median"   "quantile" "setNames" "symnum"  

$`package:Stringendo`
 [1] "extPNG"          "FixPath"         "FixPlotName"     "flag.nameiftrue" "idate"          
 [6] "kpp"             "kpps"            "kppu"            "ppp"             "sppp"           

$`package:utils`
[1] "head"

.GlobalEnv
c("Seurat.utils", "CodeAndRoll2")
c("Seurat.utils", "ggExpress")
c("Seurat.utils", "ggplot2")
c("Seurat.utils", "ggpubr")
c("Seurat.utils", "graphics")
c("Seurat.utils", "MarkdownHelpers")
c("Seurat.utils", "Seurat", "SeuratObject")
c("Seurat.utils", "Seurat")
c("Seurat.utils", "SeuratObject", "base")
c("Seurat.utils", "stats")
c("Seurat.utils", "Stringendo")
c("SeuratObject", "base")
c("sp", "base")
character(0)
base
CodeAndRoll2
ggplot2
ggpubr
graphics
grDevices
MarkdownHelpers
methods
Seurat.utils
stats
Stringendo
utils