Merge

.Rbuildignore

@@ -8,3 +8,4 @@
 ^doc$
 ^Meta$
 ^\.github$
+^data-raw$

DESCRIPTION

@@ -1,20 +1,23 @@
 Package: FLAMES
 Type: Package
 Title: FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data
-Version: 1.7.2
-Date: 2022-4-21
-Authors@R: c(person("Luyi", "Tian", role=c("aut"),
-                    email="tian.l@wehi.edu.au"),
-             person("Oliver", "Voogd", role=c("aut", "cre"),
-                    email="voogd.o@wehi.edu.au"),
-             person("Jakob", "Schuster", role=c("aut"),
-		    email="schuster.j@wehi.edu.au"),
-	     person("Changqing", "Wang", role=c("aut"),
-		    email="wang.ch@wehi.edu.au"),
-	     person("Shian",  "Su", role=c("aut"),
-                    email="su.s@wehi.edu.au"),
-             person("Matthew", "Ritchie",role=c("ctb"),
-                    email="mritchie@wehi.edu.au"))
+Version: 1.7.3
+Date: 2023-10-2
+Authors@R: c(
+       person("Luyi", "Tian", role=c("aut"),
+              email="tian.l@wehi.edu.au"),
+       person("Changqing", "Wang", role=c("aut"),
+              email="wang.ch@wehi.edu.au"),
+       person("Youpei", "You", role=c("aut"),
+              email="you.yu@wehi.edu.au"),
+       person("Oliver", "Voogd", role=c("aut", "cre"),
+              email="voogd.o@wehi.edu.au"),
+       person("Jakob", "Schuster", role=c("aut"),
+              email="schuster.j@wehi.edu.au"),
+       person("Shian",  "Su", role=c("aut"),
+              email="su.s@wehi.edu.au"),
+       person("Matthew", "Ritchie",role=c("ctb"),
+              email="mritchie@wehi.edu.au"))
 Description: Semi-supervised isoform detection and annotation from both bulk and single-cell 
   long read RNA-seq data. Flames provides automated pipelines for analysing isoforms,
   as well as intermediate functions for manual execution.
@@ -65,6 +68,7 @@ Imports:
     withr,
     zlibbioc,
     future,
+    methods
 Suggests: 
     BiocStyle,
     GEOquery,
@@ -77,8 +81,11 @@ Suggests:
     uwot,
     testthat (>= 3.0.0)
 LinkingTo: Rcpp, Rhtslib, zlibbioc
-SystemRequirements: GNU make, C++11
+SystemRequirements: GNU make, C++17
 RoxygenNote: 7.2.3
 VignetteBuilder: knitr
 URL: https://github.com/OliverVoogd/FLAMES
 Config/testthat/edition: 3
+Depends: 
+    R (>= 2.10)
+LazyData: true

NAMESPACE

@@ -22,7 +22,6 @@ export(plot_coverage)
 export(plot_demultiplex)
 export(quantify_transcript)
 export(sc_DTU_analysis)
-export(sc_annotate_plots)
 export(sc_heatmap_expression)
 export(sc_long_multisample_pipeline)
 export(sc_long_pipeline)
@@ -38,7 +37,6 @@ importFrom(Biostrings,readDNAStringSet)
 importFrom(Biostrings,writeXStringSet)
 importFrom(ComplexHeatmap,AnnotationFunction)
 importFrom(ComplexHeatmap,Heatmap)
-importFrom(ComplexHeatmap,HeatmapAnnotation)
 importFrom(ComplexHeatmap,columnAnnotation)
 importFrom(ComplexHeatmap,rowAnnotation)
 importFrom(DropletUtils,read10xCounts)
@@ -55,7 +53,6 @@ importFrom(GenomicRanges,granges)
 importFrom(GenomicRanges,strand)
 importFrom(GenomicRanges,width)
 importFrom(Matrix,colSums)
-importFrom(Matrix,t)
 importFrom(Matrix,tail)
 importFrom(MultiAssayExperiment,"experiments<-")
 importFrom(MultiAssayExperiment,MultiAssayExperiment)
@@ -98,22 +95,25 @@ importFrom(circlize,colorRamp2)
 importFrom(cowplot,get_legend)
 importFrom(cowplot,plot_grid)
 importFrom(dplyr,across)
+importFrom(dplyr,all_of)
 importFrom(dplyr,any_vars)
 importFrom(dplyr,filter)
 importFrom(dplyr,filter_at)
 importFrom(dplyr,group_by)
 importFrom(dplyr,groups)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
+importFrom(dplyr,select)
+importFrom(dplyr,select_if)
 importFrom(dplyr,slice_max)
 importFrom(dplyr,summarise)
 importFrom(dplyr,summarise_at)
 importFrom(dplyr,summarize_at)
 importFrom(dplyr,top_n)
+importFrom(dplyr,ungroup)
 importFrom(future,plan)
 importFrom(ggbio,autoplot)
 importFrom(ggbio,geom_alignment)
-importFrom(ggbio,xlim)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,coord_polar)
 importFrom(ggplot2,element_blank)
@@ -133,6 +133,7 @@ importFrom(ggplot2,scale_colour_gradient2)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_bw)
 importFrom(ggplot2,xlab)
+importFrom(ggplot2,xlim)
 importFrom(ggplot2,ylab)
 importFrom(grid,unit)
 importFrom(grid,viewport)
@@ -141,12 +142,11 @@ importFrom(igraph,as_adjacency_matrix)
 importFrom(jsonlite,fromJSON)
 importFrom(jsonlite,toJSON)
 importFrom(magrittr,"%>%")
-importFrom(magrittr,'%>%')
+importFrom(methods,is)
 importFrom(parallel,detectCores)
 importFrom(reticulate,dict)
 importFrom(reticulate,import_from_path)
 importFrom(rtracklayer,import)
-importFrom(rtracklayer,import.gff3)
 importFrom(scater,runUMAP)
 importFrom(scran,buildSNNGraph)
 importFrom(scran,fixedPCA)
@@ -157,7 +157,9 @@ importFrom(scuttle,addPerFeatureQC)
 importFrom(scuttle,isOutlier)
 importFrom(scuttle,logNormCounts)
 importFrom(stats,chisq.test)
+importFrom(stats,complete.cases)
 importFrom(stats,median)
+importFrom(stats,na.omit)
 importFrom(stats,quantile)
 importFrom(stats,setNames)
 importFrom(stats,weighted.mean)
@@ -169,7 +171,10 @@ importFrom(tidyr,pivot_wider)
 importFrom(utils,file_test)
 importFrom(utils,modifyList)
 importFrom(utils,read.csv)
+importFrom(utils,read.delim)
 importFrom(utils,read.table)
+importFrom(utils,setTxtProgressBar)
+importFrom(utils,txtProgressBar)
 importFrom(utils,write.csv)
 importFrom(withr,with_package)
 useDynLib(FLAMES, .registration=TRUE)

R/data.R

@@ -0,0 +1,47 @@
+#' scMixology short-read gene counts - sample 1
+#'
+#' Short-read single cell RNA-seq profiling of 
+#' human lung adenocarcinoma cell lines using 10X version 
+#' 2 chemstry. Single cells from five human lung adenocarcinoma
+#' cell lines (H2228, H1975, A549, H838 and HCC827) were mixed 
+#' in equal proportions and processed using the Chromium 10X platform, 
+#' then sequenced using Illumina HiSeq 2500. See
+#' Tian L, Dong X, Freytag S, Lê Cao KA et al. 
+#' Benchmarking single cell RNA-sequencing analysis pipelines using
+#' mixture control experiments. Nat Methods 2019 Jun;16(6):479-487. PMID: 31133762
+#'
+#'
+#' @format ## `scmixology_lib90`
+#' A \code{SingleCellExperiment}
+#' @source <https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126906>
+"scmixology_lib90"
+
+#' scMixology short-read gene counts - sample 2
+#'
+#' Short-read gene counts from long and short-read single 
+#' cell RNA-seq profiling of human  lung adenocarcinoma cell 
+#' lines using 10X version 2 chemstry. See
+#' Tian, L. et al. Comprehensive characterization of single-cell
+#' full-length isoforms in human and mouse with long-read sequencing.
+#' Genome Biology 22, 310 (2021).
+#' 
+#'
+#' @format ## `scmixology_lib10`
+#' A \code{SingleCellExperiment} with 7,240 rows and 60 columns:
+#' @source <https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE154869>
+"scmixology_lib10"
+
+
+#' scMixology long-read transcript counts - sample 2
+#'
+#' long-read transcript counts from long and short-read single 
+#' cell RNA-seq profiling of human  lung adenocarcinoma cell 
+#' lines using 10X version 2 chemstry. See
+#' Tian, L. et al. Comprehensive characterization of single-cell
+#' full-length isoforms in human and mouse with long-read sequencing.
+#' Genome Biology 22, 310 (2021).
+#'
+#' @format ## `scmixology_lib10_transcripts`
+#' A \code{SingleCellExperiment} with 7,240 rows and 60 columns:
+#' @source <https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE154869>
+"scmixology_lib10_transcripts"

R/find_barcode.R

@@ -85,6 +85,7 @@ find_barcode <- function(
   }
 }
 
+#' @importFrom utils read.delim
 convert_cellranger_bc <- function(bc_allow, bc_from, bc_to) {
   from <- read.delim(bc_from, header = FALSE)$V1
   to <- read.delim(bc_to, header = FALSE)$V1

R/sc_DTU_analysis.R

@@ -37,15 +37,17 @@
 #' The table is sorted by decreasing P-values. It will also be saved as \code{sc_DTU_analysis.csv} under the
 #' output folder.
 #'
-#' @importFrom dplyr group_by summarise_at top_n left_join summarise groups mutate filter_at any_vars
+#' @importFrom dplyr group_by ungroup summarise_at top_n left_join summarise groups mutate filter_at any_vars select_if select all_of 
 #' @importFrom tidyr gather pivot_wider as_tibble
 #' @importFrom magrittr "%>%"
 #' @importFrom S4Vectors DataFrame
 #' @importFrom SingleCellExperiment counts SingleCellExperiment colLabels colLabels<-
 #' @importFrom SummarizedExperiment rowData colData rowData<- colData<-
 #' @importFrom scuttle addPerCellQC addPerFeatureQC isOutlier
-#' @importFrom utils write.csv
-#' @importFrom stats chisq.test
+#' @importFrom utils write.csv setTxtProgressBar
+#' @importFrom stats chisq.test complete.cases na.omit
+#' @importFrom methods is
+#' @importFrom utils txtProgressBar
 #' @export
 #' @examples
 #' outdir <- tempfile()