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HelenaLC
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Jan 14, 2022
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,74 @@ | ||
| # args <- list( | ||
| # pdf = "plts/memory.pdf", | ||
| # fun = "code/utils-plotting.R", | ||
| # res = list.files("logs", ".*\\.txt", full.names = TRUE)) | ||
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| source(args$fun) | ||
| res <- lapply(args$res, read.table, header = TRUE) | ||
| mbs <- do.call(rbind, res)[["max_rss"]] | ||
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| # get metadata from output names | ||
| # rts_{reftyp}-{datset},{subset}, | ||
| # {method},{ngs},{ncs},{rep}.rds | ||
| ss <- strsplit(basename(gsub("\\.txt", "", args$res)), ",") | ||
| reftyp <- gsub("rts_([a-z])-.*", "\\1", sapply(ss, .subset, 1)) | ||
| refset <- paste(sep = ",", | ||
| gsub(".*-", "", sapply(ss, .subset, 1)), | ||
| sapply(ss, .subset, 2)) | ||
| vars <- seq(3, 6) | ||
| names(vars) <- c("method", "ngs", "ncs", "rep") | ||
| vars <- lapply(vars, \(.) sapply(ss, .subset, .)) | ||
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| df <- data.frame(mbs, reftyp, refset, vars) %>% | ||
| pivot_longer( | ||
| values_to = "n", | ||
| names_to = "dim", | ||
| cols = c("ngs", "ncs")) %>% | ||
| filter(n != "x") %>% | ||
| group_by(dim) %>% | ||
| mutate(n = factor(n, sort(as.numeric(unique(n))))) %>% | ||
| ungroup() %>% | ||
| mutate( | ||
| dim = factor(dim, | ||
| levels = c("ngs", "ncs"), | ||
| labels = c("# genes", "# cells")), | ||
| method = droplevels(factor(method, names(.methods_pal)))) %>% | ||
| group_by(method, dim, n) %>% | ||
| summarise_at("mbs", mean) | ||
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| pal <- .methods_pal[levels(df$method)] | ||
| lab <- parse(text = paste( | ||
| sep = "~", | ||
| sprintf("bold(%s)", LETTERS), | ||
| gsub("\\s", "~", names(pal)))) | ||
| anno <- mutate(df, letter = LETTERS[ | ||
| match(method, levels(method))]) | ||
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| plt <- ggplot(df, aes(factor(n), mbs, | ||
| col = method, fill = method)) + | ||
| facet_grid(~ dim, scales = "free") + | ||
| geom_bar( | ||
| width = 0.9, | ||
| stat = "identity", | ||
| position = "dodge") + | ||
| geom_text(data = anno, | ||
| aes(label = letter, y = -250), | ||
| size = 1.5, color = "black", | ||
| position = position_dodge(0.9)) + | ||
| scale_fill_manual(values = pal, labels = lab) + | ||
| scale_color_manual(values = pal, labels = lab) + | ||
| xlab(NULL) + scale_y_continuous( | ||
| "memory usage (MBs)", | ||
| limits = c(-500, 4e3), | ||
| expand = c(0, 0)) | ||
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| thm <- theme( | ||
| axis.ticks.x = element_blank(), | ||
| legend.title = element_blank(), | ||
| legend.text = element_text(hjust = 0), | ||
| panel.grid.major.y = element_line(color = "grey")) | ||
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| fig <- .prettify(plt, thm) | ||
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| saveRDS(fig, args$rds) | ||
| ggsave(args$pdf, fig, width = 18, height = 9, units = "cm") |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| # args <- list( | ||
| # rds = list.files("plts", "mbs.*\\.rds", full.names = TRUE), | ||
| # pdf = "figs/memory.pdf", | ||
| # uts = "code/utils-plotting.R") | ||
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| source(args$uts) | ||
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| ps <- lapply(args$rds, readRDS) | ||
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| pat <- paste0("_", c("n", "b", "k"), ".rds") | ||
| ps <- ps[sapply(pat, grep, args$rds)] | ||
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| fig <- wrap_plots(ps, ncol = 1) + | ||
| plot_annotation(tag_levels = "a") & | ||
| theme( | ||
| plot.margin = margin(), | ||
| panel.spacing = unit(1, "mm"), | ||
| legend.title = element_blank(), | ||
| plot.tag = element_text(size = 9, face = "bold")) | ||
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| ggsave(args$pdf, fig, width = 18, height = 16, units = "cm") |