## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", error = FALSE, warning = FALSE, message = FALSE, crop = NULL ) stopifnot(requireNamespace("htmltools")) htmltools::tagList(rmarkdown::html_dependency_font_awesome()) sce <- readRDS("sce.rds") ## ----init--------------------------------------------------------------------- library(iSEE) init <- DataFrame( Name = c("Feature assay plot 1", "Feature assay plot 2"), Width = c(6, 6) ) app <- iSEE(sce, initialPanels = init) ## ----fexArg------------------------------------------------------------------- fexArg <- featAssayPlotDefaults(sce, 2) fexArg$YAxisFeatName <- c("0610009L18Rik", "0610009B22Rik") app <- iSEE(sce, initialPanels = init, featAssayArgs = fexArg) ## ----yaxis-------------------------------------------------------------------- cdArgs <- colDataPlotDefaults(sce, 2) cdArgs$DataBoxOpen <- TRUE cdArgs$YAxis <- c("NREADS", "TOTAL_DUP") init <- DataFrame( Name = c("Column data plot 1", "Column data plot 2"), Width = c(6, 6) ) app <- iSEE(sce, initialPanels = init, colDataArgs = cdArgs) ## ----xaxis-------------------------------------------------------------------- fexArg <- featAssayPlotDefaults(sce, 4) fexArg$DataBoxOpen <- TRUE # Example 1 fexArg[1, "XAxis"] <- "None" # Example 2 fexArg[2, "XAxis"] <- "Column data" fexArg[2, "XAxisColData"] <- "Core.Type" # Example 3a fexArg[3, "XAxis"] <- "Feature name" fexArg[3, "XAxisFeatName"] <- "Zyx" # Example 3b (also requires a row statistic table) fexArg[4, "XAxis"] <- "Feature name" fexArg[4, "XAxisRowTable"] <- "Row statistics table 1" rowData(sce)[, "gene_id"] <- rownames(sce) rsArg <- rowStatTableDefaults(sce, 1) rsArg$Selected <- "Ints2" rsArg$SearchColumns <- list(gene_id="Ints") # Initialisation init <- DataFrame( Name = c( paste("Feature assay plot", 1:4), "Row statistics table 1"), Width = c(rep(6, 4), 12) ) app <- iSEE(sce, initialPanels = init, featAssayArgs = fexArg, rowStatArgs = rsArg) ## ----redDimPlotDefaults-type-------------------------------------------------- rdArgs <- redDimPlotDefaults(sce, 1) rdArgs$DataBoxOpen <- TRUE rdArgs$Type <- "TSNE" rdArgs$XAxis <- 2 rdArgs$YAxis <- 1 init <- DataFrame( Name = c("Reduced dimension plot 1"), Width = c(6) ) app <- iSEE(sce, initialPanels = init, redDimArgs = rdArgs) ## ----featAssayPlotDefaults-assay---------------------------------------------- fexArg <- featAssayPlotDefaults(sce, 2) fexArg$DataBoxOpen <- TRUE fexArg$Assay <- c("rsem_counts", "tophat_counts") init <- DataFrame( Name = paste("Feature assay plot", 1:2), Width = c(6, 6) ) app <- iSEE(sce, initialPanels = init, featAssayArgs = fexArg) ## ----ColorByDefaultColor------------------------------------------------------ cdArgs <- colDataPlotDefaults(sce, 2) cdArgs$VisualBoxOpen <- TRUE cdArgs$VisualChoices <- list(c("Color", "Points", "Other"), c("Color", "Points", "Other")) cdArgs$ColorByDefaultColor[2] <- c("chocolate3") cdArgs$PointAlpha[2] <- 0.2 cdArgs$PointSize[2] <- 2 cdArgs$Downsample[2] <- TRUE cdArgs$SampleRes[2] <- 150 cdArgs$FontSize[2] <- 2 init <- DataFrame( Name = c("Column data plot 1", "Column data plot 2"), Width = c(6, 6) ) app <- iSEE(sce, initialPanels = init, colDataArgs = cdArgs) ## ----aesthetic-covariate------------------------------------------------------ cdArgs <- colDataPlotDefaults(sce, 2) cdArgs$VisualBoxOpen <- TRUE cdArgs$VisualChoices <- list(c("Color", "Shape"), c("Color", "Shape")) cdArgs$ColorBy <- "Column data" cdArgs$ShapeBy <- "Column data" cdArgs$ColorByColData <- c("Core.Type", "TOTAL_DUP") cdArgs$ShapeByColData <- c("Core.Type", "driver_1_s") init <- DataFrame( Name = c("Column data plot 1", "Column data plot 2"), Width = c(6, 6) ) app <- iSEE(sce, initialPanels = init, colDataArgs = cdArgs) ## ----facet-------------------------------------------------------------------- cdArgs <- colDataPlotDefaults(sce, 3) cdArgs$VisualBoxOpen <- TRUE cdArgs$VisualChoices <- list("Facets", "Facets", "Facets") cdArgs$FacetByRow <- c(TRUE, FALSE, TRUE) cdArgs$FacetByColumn <- c(FALSE, TRUE, TRUE) cdArgs$RowFacetByColData <- "driver_1_s" cdArgs$ColumnFacetByColData <- "Core.Type" init <- DataFrame( Name = paste("Column data plot", 1:3), Width = c(4, 4, 4) ) app <- iSEE(sce, initialPanels = init, colDataArgs = cdArgs) ## ----select-brish------------------------------------------------------------- # Preconfigure the receiver panel cdArgs <- colDataPlotDefaults(sce, 1) cdArgs$SelectBoxOpen <- TRUE cdArgs$SelectByPlot <- "Reduced dimension plot 1" cdArgs$SelectEffect <- "Color" cdArgs$SelectColor <- "darkgoldenrod1" # Preconfigure the sender panel, including the point selection rdArgs <- redDimPlotDefaults(sce, 1) rdArgs$BrushData <- list( list(xmin = 2.8, xmax = 10.4, ymin = 0.6, ymax = 13.2, mapping = list(x = "X", y = "Y"), domain = list(left = -14.0, right = 10.9, bottom = -12.0, top = 16.4), range = list(left = 38.7, right = 541.5, bottom = 466.0, top = 23.7), log = list(x = NULL, y = NULL), direction = "xy", brushId = "redDimPlot1_Brush", outputId = "redDimPlot1") ) init <- DataFrame( Name = c("Reduced dimension plot 1", "Column data plot 1"), Width = c(6, 6) ) app <- iSEE(sce, initialPanels = init, redDimArgs = rdArgs, colDataArgs = cdArgs) ## ----select-lasso------------------------------------------------------------- # Preconfigure the receiver panel cdArgs <- colDataPlotDefaults(sce, 1) cdArgs$SelectBoxOpen <- TRUE cdArgs$SelectByPlot <- "Reduced dimension plot 1" cdArgs$SelectEffect <- "Color" cdArgs$SelectColor <- "darkgoldenrod1" # Preconfigure the sender panel, including the point selection rdArgs <- redDimPlotDefaults(sce, 1) rdArgs$LassoData <- list( list(lasso = NULL, closed = TRUE, panelvar1 = NULL, panelvar2 = NULL, mapping = list( x = "X", y = "Y"), coord = structure(c(9.7, 4.0, 2.0, 8.2, 10.5, 9.7, 9.0, 12.8, 7.9, 0.9, 2.1, 9.0), .Dim = c(6L, 2L))) ) init <- DataFrame( Name = c("Reduced dimension plot 1", "Column data plot 1"), Width = c(6, 6) ) app <- iSEE(sce, initialPanels = init, redDimArgs = rdArgs, colDataArgs = cdArgs) ## ----integer------------------------------------------------------------------ fexArg <- featAssayPlotDefaults(sce, 2) fexArg$DataBoxOpen <- TRUE fexArg$Assay <- c(6, 6) fexArg$YAxisFeatName <- c(10, 11) fexArg$XAxis <- "Feature name" fexArg$XAxisFeatName <- c(12, 13) init <- DataFrame( Name = paste("Feature assay plot", 1:2), Width = c(6, 6) ) app <- iSEE(sce, initialPanels = init, featAssayArgs = fexArg) ## ----character-integer-------------------------------------------------------- fexArg <- featAssayPlotDefaults(sce, 2) fexArg$DataBoxOpen <- TRUE fexArg$Assay <- c(6, "counts") init <- DataFrame( Name = paste("Feature assay plot", 1:2), Width = c(6, 6) ) app <- iSEE(sce, initialPanels = init, featAssayArgs = fexArg) ## ----character---------------------------------------------------------------- fexArg <- featAssayPlotDefaults(sce, 2) fexArg$DataBoxOpen <- TRUE fexArg$Assay <- c("logcounts", "counts") fexArg$YAxisFeatName <- c("A3galt2", "A4galt") fexArg$XAxis <- "Feature name" fexArg$XAxisFeatName <- c("L3mbtl1", "L3mbtl2") init <- DataFrame( Name = paste("Feature assay plot", 1:2), Width = c(6, 6) ) app <- iSEE(sce, initialPanels = init, featAssayArgs = fexArg) ## ----------------------------------------------------------------------------- introtour <- read.delim( system.file("extdata/intro_firststeps.txt", package = "iSEE"), sep = ";", header = TRUE) head(introtour) ## ----sessioninfo-------------------------------------------------------------- sessionInfo() # devtools::session_info()