## ----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()) sce <- readRDS("sce.rds") ## ----eval=!exists("SCREENSHOT"), include=FALSE-------------------------------- # SCREENSHOT <- function(x, ...) knitr::include_graphics(x, dpi = NA) ## ----echo=FALSE, out.width='50%', fig.align='center'-------------------------- knitr::include_graphics(path = system.file(package="iSEE", "www/iSEE.png", mustWork=TRUE)) ## ----------------------------------------------------------------------------- library(iSEE) app <- iSEE(sce, initial=list( ReducedDimensionPlot(), ColumnDataPlot() )) ## ----echo=FALSE--------------------------------------------------------------- SCREENSHOT("screenshots/links-multi-naive.png") ## ----echo=FALSE--------------------------------------------------------------- rdp <- ReducedDimensionPlot() cdp <- ColumnDataPlot( YAxis="NREADS", XAxis="Column data", XAxisColumnData="dissection_s", ColumnSelectionSource="ReducedDimensionPlot1", SelectionBoxOpen=TRUE) app <- iSEE(sce, initial=list(rdp, cdp)) ## ----echo=FALSE--------------------------------------------------------------- SCREENSHOT("screenshots/links-multi-unselected.png") ## ----echo=FALSE--------------------------------------------------------------- brush <- list(xmin = -45.943219326064, xmax = -0.9320051164658, ymin = -70.389479254644, ymax = -5.1362394173266, coords_css = list(xmin = 51.009614944458, xmax = 219.009614944458, ymin = 233.009613037109, ymax = 463.856708268114), coords_img = list(xmin = 66.3132158276913, xmax = 284.715575288405, ymin = 302.912485837478, ymax = 603.013698630137), img_css_ratio = list(x = 1.30001404440901, y = 1.29999995231628), mapping = list(x = "X", y = "Y"), domain = list(left = -49.1019902822795, right = 57.2288623709446, bottom = -70.389479254644, top = 53.5190834641121), range = list(left = 50.986301369863, right = 566.922374429224, bottom = 603.013698630137, top = 33.1552511415525), log = list(x = NULL, y = NULL), direction = "xy", brushId = "ReducedDimensionPlot1_Brush", outputId = "ReducedDimensionPlot1") rdp <- ReducedDimensionPlot(BrushData=brush) app <- iSEE(sce, initial=list(rdp, cdp)) ## ----echo=FALSE--------------------------------------------------------------- SCREENSHOT("screenshots/links-multi-brushed.png") ## ----echo=FALSE--------------------------------------------------------------- lasso <- list(lasso = NULL, closed = TRUE, panelvar1 = NULL, panelvar2 = NULL, mapping = list( x = "X", y = "Y"), coord = structure(c(24.7886887175902, 24.7886887175902, 43.0075135167132, 53.1886214926936, 53.4565453867984, 53.7244692809032, 39.2565789992467, 23.4490692470664, 24.7886887175902, -8.24559471370669, -26.3363891653729, -39.0564790142006, -45.5578582702682, -23.5097025323, -3.44022743748286, 15.7812416674124, -0.896209467717313, -8.24559471370669 ), .Dim = c(9L, 2L))) app <- iSEE(sce, initial=list(ReducedDimensionPlot(BrushData=lasso), cdp)) ## ----echo=FALSE--------------------------------------------------------------- SCREENSHOT("screenshots/links-multi-lasso.png") ## ----echo=FALSE--------------------------------------------------------------- cdp2 <- cdp cdp2[["ColorBy"]] <- "Column selection" app <- iSEE(sce, initial=list(rdp, cdp2)) ## ----echo=FALSE--------------------------------------------------------------- SCREENSHOT("screenshots/links-multi-color.png") ## ----echo=FALSE--------------------------------------------------------------- cdp2 <- cdp cdp2[["ColumnSelectionRestrict"]] <- TRUE app <- iSEE(sce, initial=list(rdp, cdp2)) ## ----echo=FALSE--------------------------------------------------------------- SCREENSHOT("screenshots/links-multi-restrict.png") ## ----echo=FALSE--------------------------------------------------------------- cdt <- ColumnDataTable(ColumnSelectionSource="ReducedDimensionPlot1", SelectionBoxOpen=TRUE, PanelWidth=8L) app <- iSEE(sce, initial=list(rdp, cdt)) ## ----echo=FALSE--------------------------------------------------------------- SCREENSHOT("screenshots/links-multi-table.png") ## ----echo=FALSE--------------------------------------------------------------- app <- iSEE(sce, initial=list( ColumnDataTable(PanelWidth=8L, Search="L6a"), ReducedDimensionPlot(ColumnSelectionSource="ColumnDataTable1") )) ## ----echo=FALSE--------------------------------------------------------------- SCREENSHOT("screenshots/links-multi-table2.png") ## ----echo=FALSE--------------------------------------------------------------- rdp <- ReducedDimensionPlot(SelectionBoxOpen=TRUE, SelectionHistory=list(brush, lasso)) app <- iSEE(sce, initial=list(rdp, cdp)) ## ----echo=FALSE--------------------------------------------------------------- SCREENSHOT("screenshots/links-multi-saved.png") ## ----echo=FALSE--------------------------------------------------------------- rdp <- ReducedDimensionPlot(VisualBoxOpen=TRUE, ColorByFeatureSource="RowDataTable1", ColorBy="Feature name") rdt <- RowDataTable(Search="Neuro", Selected="Neurod1") app <- iSEE(sce, initial=list(rdt, rdp)) ## ----echo=FALSE--------------------------------------------------------------- SCREENSHOT("screenshots/links-single-color.png") ## ----echo=FALSE--------------------------------------------------------------- fap <- FeatureAssayPlot(DataBoxOpen=TRUE, YAxisFeatureSource="RowDataTable1", XAxis="Column data", XAxisColumnData="dissection_s") app <- iSEE(sce, initial=list(rdt, fap)) ## ----echo=FALSE--------------------------------------------------------------- SCREENSHOT("screenshots/links-single-yaxis.png") ## ----echo=FALSE--------------------------------------------------------------- cdt <- ColumnDataTable() rdp <- ReducedDimensionPlot(VisualBoxOpen=TRUE, ColorBySampleSource="ColumnDataTable1", ColorBy="Sample name") app <- iSEE(sce, initial=list(cdt, rdp)) ## ----echo=FALSE--------------------------------------------------------------- SCREENSHOT("screenshots/links-single-sample.png") ## ----echo=FALSE--------------------------------------------------------------- BB <- list(xmin = 7.9644610460621, xmax = 10.11596038509, ymin = 24.542997535857, ymax = 26.582843087131, coords_css = list(xmin = 232.009614944458, xmax = 280.009614944458, ymin = 66.0096168518066, ymax = 95.0096168518066), coords_img = list(xmin = 301.615757865723, xmax = 364.016431997355, ymin = 85.8124987597648, ymax = 123.512497376937), img_css_ratio = list(x = 1.30001404440901, y = 1.29999995231628), mapping = list(x = "X", y = "Y"), domain = list(left = -0.814852879170668, right = 17.111910462584, bottom = -1.40152310296966, top = 29.4319851623629), range = list(left = 46.986301369863, right = 566.922374429224, bottom = 603.013698630137, top = 33.1552511415525), log = list(x = NULL, y = NULL), direction = "xy", brushId = "RowDataPlot1_Brush", outputId = "RowDataPlot1") rdpX <- RowDataPlot(YAxis="var_log", XAxis="Row data", XAxisRowData="mean_log", BrushData=BB) rdp <- ReducedDimensionPlot(VisualBoxOpen=TRUE, ColorByFeatureSource="RowDataPlot1", ColorBy="Feature name") app <- iSEE(sce, initial=list(rdpX, rdp)) ## ----echo=FALSE--------------------------------------------------------------- SCREENSHOT("screenshots/links-single-plot2plot.png") ## ----echo=FALSE--------------------------------------------------------------- initial <- list( ReducedDimensionPlot(SelectionBoxOpen=TRUE, ColumnSelectionDynamicSource=TRUE ), FeatureAssayPlot(SelectionBoxOpen=TRUE, ColumnSelectionDynamicSource=TRUE, XAxis="Column data", XAxisColumnData="dissection_s" ), ColumnDataPlot(SelectionBoxOpen=TRUE, YAxis="NREADS", ColumnSelectionDynamicSource=TRUE, XAxis="Column data", XAxisColumnData="Core.Type" ) ) app <- iSEE(sce, initial=initial) ## ----echo=FALSE--------------------------------------------------------------- SCREENSHOT("screenshots/links-dynamic-multi.png") ## ----echo=FALSE--------------------------------------------------------------- initial <- list( ReducedDimensionPlot(SelectionBoxOpen=TRUE, ColumnSelectionDynamicSource=TRUE, BrushData=brush ), FeatureAssayPlot(SelectionBoxOpen=TRUE, ColumnSelectionDynamicSource=TRUE, ColumnSelectionSource="ReducedDimensionPlot1", XAxis="Column data", XAxisColumnData="dissection_s" ), ColumnDataPlot(SelectionBoxOpen=TRUE, YAxis="NREADS", ColumnSelectionDynamicSource=TRUE, ColumnSelectionSource="ReducedDimensionPlot1", XAxis="Column data", XAxisColumnData="Core.Type" ) ) app <- iSEE(sce, initial=initial) ## ----echo=FALSE--------------------------------------------------------------- SCREENSHOT("screenshots/links-dynamic-multi2.png") ## ----echo=FALSE--------------------------------------------------------------- initial <- list( RowDataTable(), RowDataPlot(YAxis="var_log", XAxis="Row data", XAxisRowData="mean_log", BrushData=BB), FeatureAssayPlot(DataBoxOpen=TRUE, YAxisFeatureDynamicSource=TRUE, YAxisFeatureSource="RowDataPlot1", XAxis="Column data", XAxisColumnData="dissection_s" ) ) app <- iSEE(sce, initial=initial) ## ----echo=FALSE--------------------------------------------------------------- SCREENSHOT("screenshots/links-dynamic-single.png") ## ----sessioninfo-------------------------------------------------------------- sessionInfo()