## ---- echo = FALSE------------------------------------------------------------ knitr::opts_chunk$set( collapse = TRUE, comment = '>', fig.align = 'center', fig.show = 'hold' ) ## ---- echo=FALSE-------------------------------------------------------------- library(linbin) ## ----------------------------------------------------------------------------- e <- simple ## ---- echo = FALSE, results = 'asis'------------------------------------------ knitr::kable(e) ## ---- results = 'asis'-------------------------------------------------------- bins <- seq_events(event_range(e), length.out = 5) e.bins <- sample_events(e, bins, list(mean, "x"), list(mean, "y", by = "factor", na.rm = TRUE)) ## ---- echo = FALSE, results = 'asis'------------------------------------------ row.names(e.bins) = NULL knitr::kable(e.bins) ## ---- fig.width = 4, fig.height = 4------------------------------------------- plot_events(e.bins, xticks = axTicks, border = par("bg")) ## ----------------------------------------------------------------------------- events(from = c(0, 15, 25), to = c(10, 30, 35), x = 1, y = c('a', 'b', 'c')) ## ----------------------------------------------------------------------------- as_events(1:3) # vector as_events(cbind(1:3, 2:4)) # matrix as_events(data.frame(start = 1:3, x = 1, stop = 2:4), "start", "stop") # data.frame ## ---- echo = FALSE, fig.width = 4, fig.height = 4----------------------------- metrics <- rbind( cbind(event_range(e), n = 1, g = 1), cbind(event_coverage(e, closed = FALSE), n = 1, g = 2), cbind(event_overlaps(e), g = 4), cbind(event_gaps(e), n = 1, g = 3)) plot_events(metrics, group.col = "g", data.cols = "n", dim = c(4, 1), xlim = c(0, 100), col = 'grey', main = c("Range", "Coverage", "Overlaps", "Gaps"), lwd = 0.5, mar = rep(1.5, 4), oma = rep(1, 4)) ## ----------------------------------------------------------------------------- e <- elwha ## ----------------------------------------------------------------------------- bins <- event_overlaps(e) ## ---- fig.width = 4.5, fig.height = 1.25-------------------------------------- e.bins <- sample_events(e, bins, list(weighted.mean, "mean.width", "unit.length"), scaled.cols = "unit.length") plot_events(e.bins, data.cols = "mean.width", col = "grey", border = "#666666", ylim = c(0, 56), main = "", oma = rep(0, 4), mar = rep(0, 4), xticks = NA, yticks = NA) ## ----------------------------------------------------------------------------- bins <- seq_events(event_range(e), length.out = 33) ## ---- echo = FALSE, fig.width = 4.5, fig.height = 1.25------------------------ e.bins <- sample_events(e, bins, list(weighted.mean, "mean.width", "unit.length"), scaled.cols = "unit.length") plot_events(e.bins, data.cols = "mean.width", col = "grey", border = "#666666", ylim = c(0, 56), main = "", oma = rep(0, 4), mar = rep(0, 4), xticks = NA, yticks = NA) ## ----------------------------------------------------------------------------- bins <- seq_events(event_coverage(e), length.out = 20) ## ---- echo = FALSE, fig.width = 4.5, fig.height = 1.25------------------------ e.bins <- sample_events(e, bins, list(weighted.mean, "mean.width", "unit.length"), scaled.cols = "unit.length") plot_events(e.bins, data.cols = "mean.width", col = "grey", border = "#666666", ylim = c(0, 56), main = "", oma = rep(0, 4), mar = rep(0, 4), xticks = NA, yticks = NA) ## ----------------------------------------------------------------------------- e.filled <- fill_event_gaps(e, max.length = 1) # fill small gaps first bins <- seq_events(event_coverage(e.filled), length.out = 20, adaptive = TRUE) ## ---- echo = FALSE, fig.width = 4.5, fig.height = 1.25------------------------ e.bins <- sample_events(e, bins, list(weighted.mean, "mean.width", "unit.length"), scaled.cols = "unit.length") plot_events(e.bins, data.cols = "mean.width", col = "grey", border = "#666666", ylim = c(0, 56), main = "", oma = rep(0, 4), mar = rep(0, 4), xticks = NA, yticks = NA) ## ----------------------------------------------------------------------------- e <- simple bins <- seq_events(event_range(e), length.out = 1) ## ----------------------------------------------------------------------------- e.bins <- sample_events(e, bins, list(sum, c('x', 'y'), na.rm = TRUE), scaled.cols = c('x', 'y')) ## ---- echo = FALSE, results = 'asis'------------------------------------------ row.names(e.bins) = NULL knitr::kable(e.bins) ## ----------------------------------------------------------------------------- e.bins <- sample_events(e, bins, list(weighted.mean, 'x', 'y', na.rm = TRUE)) ## ---- echo = FALSE, results = 'asis'------------------------------------------ row.names(e.bins) = NULL knitr::kable(e.bins) ## ----------------------------------------------------------------------------- fun <- function(x) paste0(unique(x), collapse = '.') e.bins <- sample_events(e, bins, list(fun, 'factor')) ## ---- echo = FALSE, results = 'asis'------------------------------------------ row.names(e.bins) = NULL knitr::kable(e.bins) ## ----fig.height = 4, fig.width = 5-------------------------------------------- e <- simple bins <- seq_events(event_range(e), length.out = c(16, 4, 2)) # appends a "group" column e.bins <- sample_events(e, bins, list(sum, c('x', 'y'), na.rm = TRUE)) plot_events(e.bins, group.col = 'group')