remove sc_annotate_plots; move scmixology1.R

.Rbuildignore

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

DESCRIPTION

@@ -86,3 +86,6 @@ 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)
@@ -117,7 +114,6 @@ 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)
@@ -137,6 +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)
@@ -145,13 +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)
@@ -179,6 +174,7 @@ 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/sc_DTU_analysis.R

@@ -47,6 +47,7 @@
 #' @importFrom utils write.csv setTxtProgressBar
 #' @importFrom stats chisq.test complete.cases na.omit
 #' @importFrom methods is
+#' @importFrom utils txtProgressBar
 #' @export
 #' @examples
 #' outdir <- tempfile()