Create .gitignore

.gitignore

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+
+*.amb
+*.ann
+*.bwt
+*.pac
+*.sa

scripts/vigeas-nanopore-depth-coverage-GPDWIN4.R

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+# vigeas-depth-coverage
+# --> updated: 21 Dec 2022
+# ----> Laise de Moraes [https://lpmor22.github.io/]
+# ------> Khouri Lab, Gonçalo Moniz Institute, FIOCRUZ, Brazil
+
+if(!interactive()) pdf(NULL)
+
+library("cowplot")
+library("dplyr")
+library("ggplot2")
+library("patchwork")
+library("plyr")
+library("readr")
+library("svglite")
+
+args <- commandArgs(TRUE)
+id_sample <- args[3]
+output <- args[4]
+print(args)
+
+input_depth <- read.delim(args[1], header = FALSE)
+depth_coverage <- data.frame(position = input_depth$V2, depth = input_depth$V3)
+
+depcov1 <- ggplot() +
+ geom_line(data = depth_coverage, aes(x = position, y = depth), linewidth = .4, colour = "#000000") +
+ labs(title = paste0(id_sample),
+ y = "Per base coverage (x)", x = NULL) +
+ scale_x_continuous(breaks = c(1, 1000, 5000, 10000, 15000, 20000, 25000, 29903),
+ expand = expansion(0, 0), limits = c(0, 30000)) +
+ scale_y_continuous(expand = expansion(0, 0)) +
+ theme_light(base_size = 10) +
+ scale_y_log10(
+# labels = scales::trans_format("log10", scales::math_format(10^.x)),
+ breaks = scales::trans_breaks("log10", function(x) 10^x)) +
+ theme(plot.title = element_text(hjust = 0.5, size = 16, face = "bold"),
+ axis.title.y = element_text(angle = 90, size = 12),
+ axis.text.x = element_text(size = 8),
+ axis.text.y = element_text(hjust = 1, size = 8)) +
+ geom_hline(yintercept = 20, linetype = "dotted", colour = "#5A5A5A")
+
+output1 <- paste0(output, ".coverage.pdf")
+save_plot(output1, plot1, base_height = 4, base_width = 16)

scripts/vigeas-nanopore-sars2-depth-coverage-GPDWIN4.R

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+# vigeas-depth-coverage
+# --> updated: 21 Dec 2022
+# ----> Laise de Moraes [https://lpmor22.github.io/]
+# ------> Khouri Lab, Gonçalo Moniz Institute, FIOCRUZ, Brazil
+
+if(!interactive()) pdf(NULL)
+
+library("cowplot")
+library("dplyr")
+library("ggplot2")
+library("patchwork")
+library("plyr")
+library("readr")
+library("svglite")
+
+args <- commandArgs(TRUE)
+id_sample <- args[2]
+output <- args[3]
+print(args)
+
+input_depth <- read.delim(args[1], header = FALSE)
+depth_coverage <- data.frame(position = input_depth$V2, depth = input_depth$V3)
+
+# https://www.ncbi.nlm.nih.gov/nuccore/1798174254
+# https://doi.org/10.1038/s41586-020-2286-9
+map1 <- tribble(~"class", ~"gene", ~"start", ~"end",
+ "UTR", "5'UTR", 1, 265,
+ "ORFs", "ORF1a", 266, 13468,
+ "ORFs", "ORF1b", 13468, 21555,
+ "Structural proteins", "S", 21563, 25384,
+ "Structural proteins", "E", 26245, 26472,
+ "Structural proteins", "M", 26523, 27191,
+ "Structural proteins", "N", 28274, 29533,
+ "UTR", "3'UTR", 29675, 29903)
+map2 <- tribble(~"class", ~"gene", ~"start", ~"end",
+ "NSPs", "nsp1", 266, 805,
+ "NSPs", "nsp2", 806, 2719,
+ "NSPs", "nsp3", 2720, 8554,
+ "NSPs", "nsp4", 8555, 10054,
+ "NSPs", "nsp5", 10055, 10972,
+ "NSPs", "nsp6", 10973, 11842,
+ "NSPs", "nsp8", 12092, 12685,
+ "NSPs", "nsp10", 13025, 13441,
+ "NSPs", "nsp12", 13442, 16236,
+ "NSPs", "nsp13", 16237, 18039,
+ "NSPs", "nsp14", 18040, 19620,
+ "NSPs", "nsp15", 19621, 20658,
+ "NSPs", "nsp16", 20659, 21552,
+ "Accessory factors", "3ab", 25393, 26220,
+ "Accessory factors", "6", 27202, 27387,
+ "Accessory factors", "7a", 27394, 27759,
+ "Accessory factors", "7b", 27756, 27887,
+ "Accessory factors", "8", 27894, 28259,
+ "Accessory factors", "9b", 28284, 28577,
+ "Accessory factors", "10", 29558, 28674)
+map3 <- tribble(~"class", ~"gene", ~"start", ~"end",
+ "NSPs", "nsp7", 11843, 12091,
+ "NSPs", "nsp9", 12686, 13024,
+ "NSPs", "nsp11", 13442, 13480)
+
+depcov1 <- ggplot() +
+ geom_line(data = depth_coverage, aes(x = position, y = depth), linewidth = .4, colour = "#000000") +
+ labs(title = paste0(id_sample),
+ y = "Per base coverage (x)", x = NULL) +
+ scale_x_continuous(breaks = c(1, 1000, 5000, 10000, 15000, 20000, 25000, 29903),
+ expand = expansion(0, 0), limits = c(0, 30000)) +
+ scale_y_continuous(expand = expansion(0, 0)) +
+ theme_light(base_size = 10) +
+ scale_y_log10(
+# labels = scales::trans_format("log10", scales::math_format(10^.x)),
+ breaks = scales::trans_breaks("log10", function(x) 10^x)) +
+ theme(plot.title = element_text(hjust = 0.5, size = 16, face = "bold"),
+ axis.title.y = element_text(angle = 90, size = 12),
+ axis.text.x = element_text(size = 8),
+ axis.text.y = element_text(hjust = 1, size = 8)) +
+ geom_hline(yintercept = 20, linetype = "dotted", colour = "#5A5A5A")
+
+map1plot <- map1 %>% ggplot() +
+ geom_rect(aes(xmin = start, xmax = end, ymin = 8, ymax = 10, fill = class),
+ linewidth = .2, colour = "#000000", alpha = .3) +
+ geom_text(aes(x = (start + end) / 2, y = 9, label = gene), size = 3) +
+ scale_x_continuous(expand = expansion(0, 0), limits = c(0, 30000)) +
+ theme_void() + theme(legend.position = "none") + coord_cartesian(clip = "off") +
+ scale_fill_manual(values = c(
+ "UTR" = "#2F67CD",
+ "ORFs" = "#FE0B12",
+ "Structural proteins" = "#11961B"))
+
+map2plot <- map2 %>% ggplot() +
+ geom_rect(aes(xmin = start, xmax = end, ymin = 8, ymax = 10, fill = class),
+ linewidth = .2, colour = "#000000", alpha = .3) +
+ geom_text(aes(x = (start + end) / 2, y = 9, label = gene), size = 3) +
+ scale_x_continuous(expand = expansion(0, 0), limits = c(0, 30000)) +
+ theme_void() + theme(legend.position = "none") + coord_cartesian(clip = "off") +
+ scale_fill_manual(values = c(
+ "NSPs" = "#FF8A8E",
+ "Accessory factors" = "#D860CF"))
+
+map3plot <- map3 %>% ggplot() +
+ geom_rect(aes(xmin = start, xmax = end, ymin = 8, ymax = 10, fill = class),
+ linewidth = .2, colour = "#000000", alpha = .3) +
+ geom_text(aes(x = (start + end) / 2, y = 9, label = gene), size = 3) +
+ scale_x_continuous(expand = expansion(0, 0), limits = c(0, 30000)) +
+ theme_void() + theme(legend.position = "none") + coord_cartesian(clip = "off") +
+ scale_fill_manual(values = c(
+ "NSPs" = "#FF8A8E"))
+
+output1 <- paste0(output, ".coverage.pdf")
+plot1 <- depcov1 / map1plot / map2plot / map3plot + plot_layout(nrow = 4, heights = c(3, .4, .3, .3))
+save_plot(output1, plot1, base_height = 5, base_width = 16)