Dev jg (GreenleafLab#40)

* update browser,anno,peakcalling * bugfix * Update GroupCoverages.R * parallel createArrow * update * update * update * updates * update documentation * update hidden functions make sure no parameters are missing a default. make sure hidden functions are not exported * addScaleDims + Bugs * updated documentation * bugfixes * bugfix * doubletUpdate * doublet * fix * finish scaleTo update * remove ... additional args unless needed * embed * update tutorial * Dev jg lsi (GreenleafLab#39) * update * update docs * update * update * CleanUp functions * update * addUMAP and addTSNE * paletteUpdate * reducedDimsOut to name * colorBy protection * updated ... to only be in function usage messages wtih ... now are .. * added installs to ArchRGenome * finalized doublet calling * finalize LSI params * bug fix ... * bugfix * bugfix * addDevMode * default prints in createArrow * bug * print update * bugfix * bug fix * bugfix dependency on h5ls * remove dependency on h5ls * update gg * update * updates * bugFixes * Update MarkerFeatures.R * bugfixes * Update HelperUtils.R * bug fix ggplot2 * update to ggGroups * bugfix * Update AllClasses.R * fix * Update GroupCoverages.R * update * update * Update CreateArrow.R * Update CreateArrow.R * update * bug * bugTest * subthreading 2 * a * order by size * bugfix * tss fix for normal values * asdas * Update CreateArrow.R * bugfix * updates * asd * Update ReproduciblePeakSet.R * Update QualityControl.R * bug * larger tss plot * plot params * Update CreateArrow.R Co-authored-by: Ryan Corces <[email protected]>
roshan9128 · Feb 6, 2020 · ca48916 · ca48916
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diff --git a/.DS_Store b/.DS_Store
diff --git a/.Rhistory b/.Rhistory
@@ -1,30 +1,335 @@
-```{r, out.width="0.3\\linewidth", include=TRUE, fig.align="center", echo=FALSE}
-knitr::include_graphics("../../images/tutorial_1_UMAP-Clusters.pdf")
-knitr::include_graphics(c("../../images/ArchRProject_Schematic.png", "../../images/ArchR_FunctionSchematic.png", "../../images/tutorial_1_UMAP-Clusters.png", "../../images/tutorial_2_tracks.pdf", "../../images/tutorial_3_MarkerGeneScores.pdf", "../../images/tutorial_4_MarkerGeneHeatmap.pdf"))
-knitr::include_graphics("../../images/tutorial_1_UMAP-Clusters.pdf")
-getwd()
-../../images/tutorial_1_UMAP-Clusters.pdf
-library(png)
-library(grid)
-library(gridExtra)
+---
+title: "ArchR Hematopoiesis Tutorial"
+author: "Jeffrey Granja"
+date: "11/22/2019"
+output: html_document
+---
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+## R Markdown
+knitr::opts_chunk$set(echo = TRUE)
+knitr::opts_chunk$set(echo = TRUE)
+summary(cars)
+plot(pressure)
+knitr::opts_chunk$set(echo = TRUE)
+setwd("~/Documents/Heme_Tutorial/")
+data("geneAnnoHg19")
+data("genomeAnnoHg19")
+threads <- 8
+pathFragments <- "Heme_Fragments"
+inputFiles <- list.files(pathFragments, pattern = ".gz", full.names = TRUE)
+names(inputFiles) <- gsub(".fragments.tsv.gz", "", list.files(pathFragments, pattern = ".gz"))
+inputFiles <- inputFiles[!grepl(".tbi", inputFiles)]
+inputFiles
+knitr::opts_chunk$set(echo = TRUE)
+#Input Libraries
 library(ArchR)
-setArchRThreads
-setArchRThreads()
-getwd()
-knitr::include_graphics(
-c(
-"../../images/ArchRProject_Schematic.png",
-"../../images/ArchR_FunctionSchematic.png",
-"../../images/tutorial_1_UMAP-Clusters.pdf",
-"../../images/tutorial_2_tracks.pdf",
-"../../images/tutorial_3_MarkerGeneScores.pdf",
-"../../images/tutorial_4_MarkerGeneHeatmap.pdf"
+#Set/Create Working Directory to Folder
+setwd("~/Documents/Heme_Tutorial/")
+#Load Genome Annotations
+data("geneAnnoHg19")
+data("genomeAnnoHg19")
+#Set Threads to be used
+threads <- 8
+pathFragments <- "Heme_Fragments"
+inputFiles <- list.files(pathFragments, pattern = ".gz", full.names = TRUE)
+names(inputFiles) <- gsub(".fragments.tsv.gz", "", list.files(pathFragments, pattern = ".gz"))
+inputFiles <- inputFiles[!grepl(".tbi", inputFiles)]
+inputFiles
+#Input Libraries
+library(ArchR)
+#Set/Create Working Directory to Folder
+setwd("~/Documents/Heme_Tutorial/")
+#Load Genome Annotations
+data("geneAnnoHg19")
+data("genomeAnnoHg19")
+#Set Threads to be used
+threads <- 8
+knitr::opts_chunk$set(echo = TRUE)
+opts_knit$set(root.dir = "~/Documents/Heme_Tutorial/")
+library(knitr)
+knitr::opts_chunk$set(echo = TRUE)
+opts_knit$set(root.dir = "~/Documents/Heme_Tutorial/")
+#Input Libraries
+library(ArchR)
+#Load Genome Annotations
+data("geneAnnoHg19")
+data("genomeAnnoHg19")
+#Set Threads to be used
+threads <- 8
+pathFragments <- "Heme_Fragments"
+inputFiles <- list.files(pathFragments, pattern = ".gz", full.names = TRUE)
+names(inputFiles) <- gsub(".fragments.tsv.gz", "", list.files(pathFragments, pattern = ".gz"))
+inputFiles <- inputFiles[!grepl(".tbi", inputFiles)]
+inputFiles
+#Input Libraries
+library(ArchR)
+#Load Genome Annotations
+data("geneAnnoHg19")
+data("genomeAnnoHg19")
+#Set Threads to be used
+threads <- 8
+library(knitr)
+knitr::opts_chunk$set(echo = TRUE)
+opts_knit$set(root.dir = "~/Documents/Heme_Tutorial/")
+#Input Libraries
+library(ArchR)
+#Load Genome Annotations
+data("geneAnnoHg19")
+data("genomeAnnoHg19")
+#Set Threads to be used
+threads <- 8
+pathFragments <- "Heme_Fragments"
+inputFiles <- list.files(pathFragments, pattern = ".gz", full.names = TRUE)
+names(inputFiles) <- gsub(".fragments.tsv.gz", "", list.files(pathFragments, pattern = ".gz"))
+inputFiles <- inputFiles[!grepl(".tbi", inputFiles)]
+inputFiles
+#Input Libraries
+library(ArchR)
+#Load Genome Annotations
+data("geneAnnoHg19")
+data("genomeAnnoHg19")
+#Set Threads to be used
+threads <- 8
+library(knitr)
+knitr::opts_chunk$set(echo = TRUE)
+opts_knit$set(root.dir = "~/Documents/Heme_Tutorial/")
+library(ArchR)
+#Input Libraries
+library(ArchR)
+#Load Genome Annotations
+data("geneAnnoHg19")
+data("genomeAnnoHg19")
+#Set Threads to be used
+threads <- 8
+pathFragments <- "Heme_Fragments"
+inputFiles <- list.files(pathFragments, pattern = ".gz", full.names = TRUE)
+names(inputFiles) <- gsub(".fragments.tsv.gz", "", list.files(pathFragments, pattern = ".gz"))
+inputFiles <- inputFiles[!grepl(".tbi", inputFiles)]
+inputFiles
+library(knitr)
+knitr::opts_chunk$set(echo = TRUE)
+opts_knit$set(root.dir = "~/Documents/Heme_Tutorial/")
+library(ArchR)
+#Load Genome Annotations
+data("geneAnnoHg19")
+data("genomeAnnoHg19")
+#Set Threads to be used
+threads <- 8
+pathFragments <- "Heme_Fragments"
+inputFiles <- list.files(pathFragments, pattern = ".gz", full.names = TRUE)
+names(inputFiles) <- gsub(".fragments.tsv.gz", "", list.files(pathFragments, pattern = ".gz"))
+inputFiles <- inputFiles[!grepl(".tbi", inputFiles)]
+inputFiles
+ArrowFiles <- createArrowFiles(
+inputFiles = inputFiles[3],
+sampleNames = names(inputFiles),
+geneAnno = geneAnnoHg19,
+genomeAnno = genomeAnnoHg19,
+threads = threads,
+force = TRUE
+)
+ArrowFiles <- createArrowFiles(
+inputFiles = inputFiles[3],
+sampleNames = names(inputFiles)[3],
+geneAnno = geneAnnoHg19,
+genomeAnno = genomeAnnoHg19,
+threads = threads,
+force = TRUE
+)
+ls
+```{r eval=TRUE, cache=TRUE}
+ArrowFiles <- createArrowFiles(
+inputFiles = inputFiles[3],
+sampleNames = names(inputFiles)[3],
+geneAnno = geneAnnoHg19,
+genomeAnno = genomeAnnoHg19,
+threads = threads,
+addGeneScoreMat = FALSE,
+addTileMat = FALSE,
+force = TRUE
 )
+knitr::opts_chunk$set(echo = TRUE)
+knitr::opts_chunk$set(eval = FALSE)
+# Small fig.width
+knitr::include_graphics("~/Documents/Heme_Tutorial/Heme_Tutorial/Plots/Plot-UMAP-TileLSI_Date-2019-11-22_Time-01-35-25.pdf")
+# Small fig.width
+knitr::include_graphics("~/Documents/Heme_Tutorial/Heme_Tutorial/Plots/Plot-UMAP-TileLSI_Date-2019-11-22_Time-01-35-25.pdf")
+# Small fig.width
+knitr::include_graphics("~/Documents/Heme_Tutorial/Heme_Tutorial/Plots/Plot-UMAP-TileLSI_Date-2019-11-22_Time-01-35-25.pdf")
+getwd()
+"/Users/jeffreygranja/Documents/Heme_Tutorial/Heme_Tutorial/Plots/Plot-UMAP-TileLSI_Date-2019-11-22_Time-01-35-25.pdf
+# Small fig.width
+knitr::include_graphics("/Users/jeffreygranja/Documents/Heme_Tutorial/Heme_Tutorial/Plots/Plot-UMAP-TileLSI_Date-2019-11-22_Time-01-35-25.pdf")
+# Small fig.width
+knitr::include_graphics("/Users/jeffreygranja/Documents/Heme_Tutorial/Heme_Tutorial/Plots/Plot-UMAP-TileLSI_Date-2019-11-22_Time-01-35-25.pdf")
+"~/Documents/HemeAll/heme/Plots/Plot-Tracks_Date-2019-11-17_Time-17-52-02.pdf"
+knitr::include_graphics(path.expand("~/Documents/HemeAll/heme/Plots/Plot-Tracks_Date-2019-11-17_Time-17-52-02.pdf"))
+file.copy
+list.files()
+list.files()
+system("cp ~/Documents/HemeAll/heme/Plots/Plot-Tracks_Date-2019-11-17_Time-17-52-02.pdf mychart.pdf")
+knitr::include_graphics(path = "mychart.pdf")
+"mychart.pdf"
+knitr::include_graphics(path = "mychart.pdf")#path.expand("~/Documents/HemeAll/heme/Plots/Plot-Tracks_Date-2019-11-17_Time-17-52-02.pdf"))
+knitr::include_graphics(path = "mychart.pdf")
+knitr::opts_chunk$set(echo = TRUE)
+```{r pressure, echo=FALSE, eval = FALSE}
+sessionInfo()
+head(sessionInfo())
+suppressPackageStartupMessages()
+Sys.info()
+.Platform
+parallel::detectCores()
+try(system("grep MemTotal /proc/meminfo", intern = TRUE), silent = TRUE)
+ram = substring(system("sysctl hw.memsize", intern = TRUE), 13) #nocov
+ram
+ram / 10^9
+as.numeric(ram) / 10^9
+get_windows_ram = function() {
+ram = try(system("grep MemTotal /proc/meminfo", intern = TRUE), silent = TRUE)
+if (class(ram) != "try-error" && length(ram) != 0) {
+ram = strsplit(ram, " ")[[1]]
+ram = as.numeric(ram[length(ram) - 1])
+ram_size = ram
+} else {
+# Fallback: This was the old method I used
+# It worked for Windows 7 and below.
+ram_size = system("wmic MemoryChip get Capacity", intern = TRUE)[-1]
+}
+return(ram_size)
+}
+system_ram = function(os) {
+if (length(grep("^linux", os))) {
+cmd = "awk '/MemTotal/ {print $2}' /proc/meminfo"
+ram = system(cmd, intern = TRUE)
+} else if (length(grep("^darwin", os))) {
+ram = substring(system("sysctl hw.memsize", intern = TRUE), 13) #nocov
+} else if (length(grep("^solaris", os))) {
+cmd = "prtconf | grep Memory" # nocov
+ram = system(cmd, intern = TRUE) ## Memory size: XXX Megabytes # nocov
+} else {
+ram = get_windows_ram() # nocov
+}
+ram
+}
+#' Get the amount of RAM
+#'
+#' Attempt to extract the amount of RAM on the current machine. This is OS
+#' specific:
+#' \itemize{
+#' \item Linux: \code{proc/meminfo}
+#' \item Apple: \code{system_profiler -detailLevel mini}
+#' \item Windows: \code{memory.size()}
+#' \item Solaris: \code{prtconf}
+#' }
+#' A value of \code{NA} is return if it isn't possible to determine the amount of RAM.
+#' @export
+#' @references The \code{print.bytes} function was taken from the \pkg{pryr} package.
+#' @examples
+#' ## Return (and pretty print) the amount of RAM
+#' get_ram()
+get_ram = function() {
+os = R.version$os
+ram = suppressWarnings(try(system_ram(os), silent = TRUE))
+if (class(ram) == "try-error" || length(ram) == 0) {
+message("\t Unable to detect your RAM. # nocov
+Please raise an issue at https://github.com/csgillespie/benchmarkme") # nocov
+ram = structure(NA, class = "ram") # nocov
+} else {
+cleaned_ram = suppressWarnings(try(clean_ram(ram, os), silent = TRUE))
+if (class(cleaned_ram) == "try-error" || length(ram) == 0) {
+message("\t Unable to detect your RAM. # nocov
+Please raise an issue at https://github.com/csgillespie/benchmarkme") # nocov
+ram = structure(NA, class = "ram") #nocov
+} else {
+ram = structure(cleaned_ram, class = "ram")
+}
+}
+return(ram)
+}
+#' @rawNamespace S3method(print,ram)
+print.ram = function(x, digits = 3, unit_system = c("metric", "iec"), ...) {
+#unit_system = match.arg(unit_system)
+unit_system = "metric"
+base = switch(unit_system, metric = 1000, iec = 1024)
+power = min(floor(log(abs(x), base)), 8)
+if (is.na(x) || power < 1) {
+unit = "B"
+} else {
+unit_labels = switch(
+unit_system,
+metric = c("kB", "MB", "GB", "TB", "PB", "EB", "ZB", "YB"),
+iec = c("KiB", "MiB", "GiB", "TiB", "PiB", "EiB", "ZiB", "YiB")
 )
-setwd("~/Documents/GitHub/ArchR/")
-library(pkdgdown)
-library(pkgdown)
-build_articles()
+unit = unit_labels[[power]]
+x = x / (base^power)
+}
+formatted = format(signif(x, digits = digits), big.mark = ",",
+scientific = FALSE, ...)
+cat(unclass(formatted), " ", unit, "\n", sep = "")
+invisible(paste(unclass(formatted), unit))
+}
+get_ram()
+plot(cars)
+```{r eval = TRUE}
+```{r}
+suppressPackageStartupMessages(library(SnapATAC))
+suppressPackageStartupMessages(library(SnapATAC))
+suppressPackageStartupMessages(library(magrittr))
+setwd("/Volumes/JG_SSD_2/Data/Analysis/Tutorial/test-snap")
+parallel::detectCores()
+Sys.Date()
 sessionInfo()
-setwd("~/Documents/Github/ArchR")
-build_site()
+#5k
+if(!file.exists("atac_pbmc_5k_nextgem_fragments.tsv.gz")){
+system("wget http://cf.10xgenomics.com/samples/cell-atac/1.2.0/atac_pbmc_5k_nextgem/atac_pbmc_5k_nextgem_fragments.tsv.gz")
+system("wget http://cf.10xgenomics.com/samples/cell-atac/1.2.0/atac_pbmc_5k_nextgem/atac_pbmc_5k_nextgem_fragments.tsv.gz.tbi")
+}
+#10k
+if(!file.exists("atac_pbmc_10k_nextgem_fragments.tsv.gz")){
+system("wget http://cf.10xgenomics.com/samples/cell-atac/1.2.0/atac_pbmc_10k_nextgem/atac_pbmc_10k_nextgem_fragments.tsv.gz")
+system("wget http://cf.10xgenomics.com/samples/cell-atac/1.2.0/atac_pbmc_10k_nextgem/atac_pbmc_10k_nextgem_fragments.tsv.gz.tbi")
+}
+#Analysis of 10x Fragment Files
+#Install pip install -user snaptools
+snapTools <- "/Users/jeffreygranja/Library/Python/2.7/bin/snaptools"
+#Fragment Files
+fragFiles <- c(
+"atac_pbmc_5k_nextgem_fragments.tsv.gz",
+"atac_pbmc_10k_nextgem_fragments.tsv.gz"
+)
+#Input Genome
+genome <- "hg19"
+if(!file.exists(paste0(genome,".chrom.sizes"))){
+system(paste0("wget http://hgdownload.cse.ucsc.edu/goldenpath/",genome,"/bigZips/",genome,".chrom.sizes"))
+}
+#Download/Set Up 10x Fragment Files
+#5k
+if(!file.exists("atac_pbmc_5k_nextgem_fragments.tsv.gz")){
+system("wget http://cf.10xgenomics.com/samples/cell-atac/1.2.0/atac_pbmc_5k_nextgem/atac_pbmc_5k_nextgem_fragments.tsv.gz")
+system("wget http://cf.10xgenomics.com/samples/cell-atac/1.2.0/atac_pbmc_5k_nextgem/atac_pbmc_5k_nextgem_fragments.tsv.gz.tbi")
+}
+#10k
+if(!file.exists("atac_pbmc_10k_nextgem_fragments.tsv.gz")){
+system("wget http://cf.10xgenomics.com/samples/cell-atac/1.2.0/atac_pbmc_10k_nextgem/atac_pbmc_10k_nextgem_fragments.tsv.gz")
+system("wget http://cf.10xgenomics.com/samples/cell-atac/1.2.0/atac_pbmc_10k_nextgem/atac_pbmc_10k_nextgem_fragments.tsv.gz.tbi")
+}
+#Analysis of 10x Fragment Files
+#Install pip install -user snaptools
+snapTools <- "/Users/jeffreygranja/Library/Python/2.7/bin/snaptools"
+#Fragment Files
+fragFiles <- c(
+"atac_pbmc_5k_nextgem_fragments.tsv.gz",
+"atac_pbmc_10k_nextgem_fragments.tsv.gz"
+)
+#Input Genome
+genome <- "hg19"
+if(!file.exists(paste0(genome,".chrom.sizes"))){
+system(paste0("wget http://hgdownload.cse.ucsc.edu/goldenpath/",genome,"/bigZips/",genome,".chrom.sizes"))
+}
+setwd("~/Documents/GitHub/ArchR")
+pkgdown::build_site()
+warnings()
+pkgdown::build_site()
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: ArchR
 Type: Package
-Date: 2019-10-17
-Title: Analyzing regulatory chromatin in R
-Version: 0.1.5
+Date: 2019-02-01
+Title: Analyzing single-cell regulatory chromatin in R.
+Version: 0.1.6
 Authors@R: c(
     person("Jeffrey", "Granja", email = "[email protected]", role = c("aut","cre")),
     person("Ryan", "Corces", role = "aut"))
@@ -11,7 +11,7 @@ Roxygen: list(markdown = TRUE)
 License: GPL (>= 2)
 LinkingTo: Rcpp
 LazyData: TRUE
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.2
 Encoding: UTF-8
 Imports:
     Rcpp (>= 0.12.16),
@@ -24,6 +24,7 @@ Imports:
     ggrepel,
     Rsamtools,
     gtable,
+    gtools,
     grid,
     gridExtra,
     Biostrings,
@@ -38,4 +39,3 @@ Depends:
     S4Vectors (>= 0.9.25),
     BiocGenerics,
     GenomicRanges,
-