## ----message=FALSE, warning=FALSE, echo=FALSE, fig.width=8.5, fig.height=6.5, eval=FALSE---- # ## Define colors # colors <- c("#e19995", "#adaf64", "#4fbe9b", "#6eb3d9", "#d098d7") # # ## Create artificial GRanges # library(GenomicRanges) # set.seed(5) # pool <- GRanges(seqnames = "chr1", # ranges = IRanges(start = sample(1:800, 120, replace = TRUE), # width = sample(25:200, 120, replace = TRUE)), # color = sample(1:5, 120, replace = TRUE)) # focal <- GRanges(seqnames = "chr1", # ranges = IRanges(start = sample(1:800, 16, replace = TRUE), # width = sample(25:200, 16, replace = TRUE)), # color = sample(1:5, 16, replace = TRUE)) # # ## Add width to metadata # pool$length <- width(pool) # focal$length <- width(focal) # # ## Match ranges # library(nullranges) # set.seed(123) # x <- matchRanges(focal = focal, # pool = pool, # covar = ~color + length, # method = 'n', replace = TRUE) # # ## Visualize sets # library(plotgardener) # library(grid) # set.seed(123) # pageCreate(width = 8.5, height = 6.5, showGuides = FALSE, xgrid = 0, ygrid = 0) # # ## Define common parameters # p <- pgParams(chrom = "chr1", chromstart = 1, chromend = 1000) # # ## Pool set # poolSet <- plotRanges(data = pool, params = p, # x = 1, y = 1, width = 2.5, height = 2.5, # fill = colors, # colorby = colorby("color")) # annoGenomeLabel(plot = poolSet, x = 1, y = 3.55) # plotText(label = "Pool Set", # x = 2.25, y = 0.9, # just = c("center", "bottom"), # fontcolor = "#33A02C", # fontface = "bold", # fontfamily = 'mono') # # ## Focal set # focalSet <- plotRanges(data = focal, params = p, # x = 5, y = 1, width = 2.5, height = 1, # fill = colors, # colorby = colorby("color")) # annoGenomeLabel(plot = focalSet, x = 5, y = 2.05) # plotText(label = "Focal Set", # x = 6.25, y = 0.9, # just = c("center", "bottom"), # fontcolor = "#1F78B4", # fontface = "bold", # fontfamily = 'mono') # # # ## Matched set # matchedSet <- plotRanges(data = matched(x), params = p, # x = 5, y = 2.5, width = 2.5, height = 1, # fill = colors, # colorby = colorby("color")) # annoGenomeLabel(plot = matchedSet, x = 5, y = 3.55) # plotText(label = "Matched Set", # x = 6.25, y = 2.75, # just = c("center", "bottom"), # fontcolor = "#A6CEE3", # fontface = "bold", # fontfamily = 'mono') # # # ## Arrow and matchRanges label # plotSegments(x0 = 3.5, y0 = 3, # x1 = 5, y1 = 3, # arrow = arrow(type = "closed", length = unit(0.1, "inches")), # fill = "black", lwd = 2) # plotText(label = "matchRanges()", fontfamily = 'mono', # x = 4.25, y = 2.9, just = c("center", "bottom")) # # # # ## Matching plots # library(ggplot2) # smallText <- theme(legend.title = element_text(size=8), # legend.text=element_text(size=8), # title = element_text(size=8), # axis.title.x = element_text(size=8), # axis.title.y = element_text(size=8)) # # plot1 <- # plotPropensity(x, sets=c('f','m','p')) + # smallText + # theme(legend.key.size = unit(0.5, 'lines'), # title = element_blank()) # # plot2 <- # plotCovariate(x=x, covar=covariates(x)[1], sets=c('f','m','p')) + # smallText + # theme(legend.text = element_blank(), # legend.position = 'none') # # plot3 <- # plotCovariate(x=x, covar=covariates(x)[2], sets=c('f','m','p'))+ # smallText + # theme(legend.key.size = unit(0.5, 'lines')) # # # ## Propensity scores # plotText(label = "plotPropensity()", # x = 1.10, y = 4.24, # just = c("left", "bottom"), # fontface = "bold", # fontfamily = 'mono') # plotText(label = "~color + length", # x = 1.25, y = 4.5, # just = c("left", "bottom"), # fontsize = 10, # fontfamily = "mono") # plotGG(plot = plot1, # x = 1, y = 4.5, width = 2.5, height = 1.5, # just = c("left", "top")) # # ## Covariate balance # plotText(label = "plotCovariate()", # x = 3.75, y = 4.24, # just = c("left", "bottom"), # fontface = "bold", # fontfamily = "mono") # plotText(label = covariates(x), # x = c(4, 5.9), y = 4.5, # just = c("left", "bottom"), # fontsize = 10, # fontfamily = "mono") # plotGG(plot = plot2, # x = 3.50, y = 4.5, width = 1.8, height = 1.5, # just = c("left", "top")) # # plotGG(plot = plot3, # x = 5.30, y = 4.5, width = 2.75, height = 1.5, # just = c("left", "top")) ## ----message=FALSE, warning=FALSE--------------------------------------------- library(nullrangesData) ## Load example data bins <- hg19_10kb_bins() bins ## ----------------------------------------------------------------------------- library(nullranges) ## Match ranges set.seed(123) mgr <- matchRanges(focal = bins[bins$looped], pool = bins[!bins$looped], covar = ~dnaseSignal + n_dnase_sites) mgr ## ----message=FALSE, warning=FALSE--------------------------------------------- library(GenomicRanges) library(plyranges) library(ggplot2) ## Summarize ctcfSignal by n_ctcf_sites mgr %>% group_by(n_ctcf_sites) %>% summarize(ctcfSignal = mean(ctcfSignal)) %>% as.data.frame() %>% ggplot(aes(x = n_ctcf_sites, y = ctcfSignal)) + geom_line() + geom_point(shape = 21, stroke = 1, fill = 'white') + theme_minimal() + theme(panel.border = element_rect(color = 'black', fill = NA)) ## ----------------------------------------------------------------------------- overview(mgr) ## ----message=FALSE------------------------------------------------------------ plotPropensity(mgr, sets = c('f', 'p', 'm'), type = 'ridges') ## ----message=FALSE, warning=FALSE, fig.height=6, fig.width=5------------------ library(patchwork) plots <- lapply(covariates(mgr), plotCovariate, x=mgr, sets = c('f', 'm', 'p')) Reduce('/', plots) ## ----------------------------------------------------------------------------- tidy_gr <- bind_ranges( looped_focal=focal(mgr), unlooped_pool=pool(mgr), unlooped_matched=mgr, .id="type" ) ## ----------------------------------------------------------------------------- cols <- c(looped_focal="#1F78B4", unlooped_matched="#A6CEE3", unlooped_pool="#33A02C") ## ----fig.width=4.5, fig.height=5---------------------------------------------- tidy_gr %>% group_by(type) %>% summarize(CTCF_occupied = 100*mean(n_ctcf_sites >= 1)) %>% as.data.frame() %>% ggplot(aes(type, CTCF_occupied, fill=type)) + geom_col(show.legend = FALSE) + ylab("CTCF occupied bins (%)") + scale_fill_manual(values=cols) + ggtitle("CTCF occupancy") ## ----------------------------------------------------------------------------- sessionInfo()