## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", error = FALSE, warning = FALSE, message = FALSE, crop = NULL ) stopifnot(requireNamespace("htmltools")) htmltools::tagList(rmarkdown::html_dependency_font_awesome()) unlink("assay.h5") ## ----eval=!exists("SCREENSHOT"), include=FALSE-------------------------------- # SCREENSHOT <- function(x, ...) knitr::include_graphics(x, dpi = NA) ## ----------------------------------------------------------------------------- library(TENxPBMCData) sce.pbmc <- TENxPBMCData("pbmc68k") sce.pbmc$Library <- factor(sce.pbmc$Library) sce.pbmc ## ----------------------------------------------------------------------------- library(scRNAseq) sce.allen <- ReprocessedAllenData("tophat_counts") class(assay(sce.allen, "tophat_counts")) ## ----------------------------------------------------------------------------- counts(sce.pbmc, withDimnames=FALSE) ## ----------------------------------------------------------------------------- object.size(counts(sce.pbmc, withDimnames=FALSE)) ## ----------------------------------------------------------------------------- first.gene <- counts(sce.pbmc)[1,] head(first.gene) ## ----------------------------------------------------------------------------- library(iSEE) app <- iSEE(sce.pbmc, initial= list(RowDataTable(Selected="ENSG00000251562", Search="MALAT1"), FeatureAssayPlot(XAxis="Column data", XAxisColumnData="Library", YAxisFeatureSource="RowDataTable1") ) ) ## ----echo=FALSE--------------------------------------------------------------- SCREENSHOT("screenshots/bigdata-hdf5.png") ## ----------------------------------------------------------------------------- sce.h5 <- sce.allen library(HDF5Array) assay(sce.h5, "tophat_counts", withDimnames=FALSE) <- writeHDF5Array(assay(sce.h5, "tophat_counts"), file="assay.h5", name="counts") class(assay(sce.h5, "tophat_counts", withDimnames=FALSE)) list.files("assay.h5") ## ----echo=FALSE--------------------------------------------------------------- unlink("assay.h5") ## ----------------------------------------------------------------------------- library(iSEE) app <- iSEE(sce.pbmc, initial= list(RowDataTable(Selected="ENSG00000251562", Search="MALAT1"), FeatureAssayPlot(XAxis="Column data", XAxisColumnData="Library", YAxisFeatureSource="RowDataTable1", VisualChoices="Point", Downsample=TRUE, VisualBoxOpen=TRUE ) ) ) ## ----echo=FALSE--------------------------------------------------------------- SCREENSHOT("screenshots/bigdata-downsample.png") ## ----eval=FALSE--------------------------------------------------------------- # panelDefaults(Downsample=TRUE) ## ----echo=FALSE--------------------------------------------------------------- brushed <- list(xmin = 0.4, xmax = 1.6672635882221, ymin = 21.106156820944, ymax = 62.899238475283, coords_css = list(xmin = 41.5274754930861, xmax = 102.504791259766, ymin = 200.009613037109, ymax = 365.009613037109), coords_img = list(xmin = 53.986301369863, xmax = 133.25766825691, ymin = 260.012487411041, ymax = 474.512479543227), img_css_ratio = list(x = 1.30001404440901, y = 1.29999995231628), mapping = list(x = "X", y = "Y", group = "GroupBy"), domain = list(left = 0.4, right = 8.6, bottom = -5.1, top = 107.1, discrete_limits = list( x = list("1", "2", "3", "4", "5", "6", "7", "8"))), range = list(left = 53.986301369863, right = 566.922374429224, bottom = 609.013698630137, top = 33.1552511415525), log = list(x = NULL, y = NULL), direction = "xy", brushId = "FeatureAssayPlot1_Brush", outputId = "FeatureAssayPlot1") library(iSEE) app <- iSEE(sce.pbmc, initial= list(RowDataTable(Selected="ENSG00000251562", Search="MALAT1"), FeatureAssayPlot(XAxis="Column data", XAxisColumnData="Library", YAxisFeatureSource="RowDataTable1", YAxisFeatureName="ENSG00000251562", VisualChoices="Point", Downsample=TRUE, VisualBoxOpen=TRUE, BrushData=brushed ) ) ) ## ----echo=FALSE--------------------------------------------------------------- SCREENSHOT("screenshots/bigdata-downsample2.png") ## ----sessioninfo-------------------------------------------------------------- sessionInfo() # devtools::session_info()