Merge pull request #5 from hsmaan/release

Release

.gitignore

@@ -15,4 +15,6 @@
 *.vcf
 *.log
 *.frq
+*.dcf
+slurm*
 

R/global.R

@@ -0,0 +1,319 @@
+library(Biostrings)
+library(DECIPHER)
+library(stringi)
+library(stringr)
+library(ape)
+library(igraph)
+library(reshape2)
+library(dplyr)
+library(uwot)
+library(RColorBrewer)
+library(ggplot2)
+library(ggthemes)
+library(plotly)
+library(ggnetwork)
+
+# Load color palettes    
+
+kev_palette <- c(
+  "dodgerblue2", "#E31A1C",
+  "green4",
+  "#6A3D9A", 
+  "#FF7F00", 
+  "black", "gold1",
+  "skyblue2", "#FB9A99", 
+  "palegreen2",
+  "#CAB2D6", 
+  "#FDBF6F", 
+  "gray70", "khaki2",
+  "maroon", "orchid1", "deeppink1", "blue1", "steelblue4",
+  "darkturquoise", "green1", "yellow4", "yellow3",
+  "darkorange4", "brown"
+)
+
+qual_palettes = brewer.pal.info[brewer.pal.info$category == "qual", ]
+qual_vector = unlist(mapply(brewer.pal, qual_palettes$maxcolors, rownames(qual_palettes)))
+
+# Functions
+
+align_get <- function(fasta, align) {
+
+  covid_seq <- readDNAStringSet(fasta)
+  if (length(covid_seq) > 10) {
+    stop("Too many sequences in fasta file, only up to 10 viral genomes allowed at a time.")
+  }
+  if (length(covid_seq) < 1) {
+    stop("No sequences found in fasta file.")
+  }
+  if (length(which((lapply(covid_seq, length)) < 29000)) > 0) {
+    stop("One or more sequences not complete (length < 29000 nucleotides).")
+  }
+  covid_align <- align
+  covid_seq <- RemoveGaps(covid_seq, removeGaps = "all", processors = NULL)
+  fasta_final <- AlignProfiles(covid_align, covid_seq)
+  return(fasta_final)
+
+}
+
+dist_get <- function(align) {
+
+  dec_dist <- dist.dna(as.DNAbin(align), model = "K80", as.matrix = TRUE, pairwise.deletion = FALSE)
+  colnames(dec_dist) <- (str_split_fixed(colnames(dec_dist), fixed("."), 2)[,1])
+  rownames(dec_dist) <- (str_split_fixed(rownames(dec_dist), fixed("."), 2)[,1])
+  return(dec_dist)
+
+}
+
+umap_process <- function(covid_dist, meta_df) {
+
+  acc_names = rownames(covid_dist)
+  covid_dist <- dist(covid_dist)
+  set.seed(2020)
+  covid_umap <- uwot::umap(covid_dist, init = "spectral", metric = "cosine", n_neighbors = 50, min_dist = 0.001, spread = 40, local_connectivity = 10)
+  covid_umap_df <- as.data.frame(covid_umap)
+  umap_df_final <- data.frame("Accession" = acc_names, "UMAP_1" = covid_umap_df[,1], "UMAP_2" = covid_umap_df[,2])
+  umap_df_final <- merge(umap_df_final, meta_df)
+  colnames(umap_df_final) <- c("Accession", "UMAP_1", "UMAP_2", "Region", "Country", "Date")
+  return(umap_df_final)
+
+}
+
+mst_graph <- function(covid_dist, meta_data) {
+
+  g <- graph.adjacency(covid_dist, mode = "undirected", weighted = TRUE, diag = FALSE)
+  g_mst <- mst(g)
+  acc_ordering <- match(meta_data[,1], names(V(g_mst)[[]]))
+  meta_ordered <- meta_data[order(acc_ordering), ]
+
+  g_mst_1 <- g_mst
+  g_mst_2 <- g_mst
+  g_mst_3 <- g_mst
+
+  meta_colors_1 <- (kev_palette[1:length(unique(meta_ordered[,(ncol(meta_ordered)-2)]))])[factor(meta_ordered[, (ncol(meta_ordered)-2)])]
+  meta_colors_2 <- (qual_vector[1:length(unique(meta_ordered[,(ncol(meta_ordered)-1)]))])[factor(meta_ordered[, (ncol(meta_ordered)-1)])]
+  color_ramp <- colorRampPalette(c("dodgerblue2", "white", "firebrick1"))(max(meta_ordered[,(ncol(meta_ordered))]))
+  meta_colors_3 <- color_ramp[meta_ordered[,(ncol(meta_ordered))]]
+
+  V(g_mst_1)$color <- meta_colors_1
+  V(g_mst_2)$color <- meta_colors_2
+  V(g_mst_3)$color <- meta_colors_3
+
+  V(g_mst_1)$Region <- meta_ordered[,(ncol(meta_ordered)-2)]
+  V(g_mst_2)$Country <- meta_ordered[,(ncol(meta_ordered)-1)]
+  V(g_mst_3)$Date <- meta_ordered[,(ncol(meta_ordered))]
+
+  lay <- layout_with_graphopt(g_mst_1, niter = 1000)
+
+  g_mst_list <- list(g_mst_1, g_mst_2, g_mst_3, lay)
+  return(g_mst_list)
+
+}
+
+snps_get <- function(alignment, metadata, positions) {
+
+  align <- alignment
+  pos <- paste(positions$Pos, positions$Gene, positions$Effect, sep = " ")
+  acc <- metadata[,1]
+  meta_vars <- metadata[,-1]
+  align_df <- as.data.frame(as.matrix(align))
+  meta_order <- match(rownames(align_df), acc)
+  align_df <- align_df[order(meta_order),]
+  align_df$m3 <- meta_vars[,3]
+  align_df$m2 <- meta_vars[,2]
+  align_df$m1 <- meta_vars[,1] # Ensure ordering, cbind() likely reorders rownames and will reorder metadata
+
+  freq_pct <- function(d_col) {
+    freq_table <- table(d_col)
+    pct_table <- as.table(sapply(freq_table, function(x) x/sum(freq_table)))
+    return(pct_table)
+  }
+
+  table_get <- function(df, position, meta_num) {
+    pos_full <- position
+    pos_num <- as.numeric(str_split_fixed(position, " ", 3)[,1][1])
+    align_pos <- df[,c(pos_num, (ncol(df) - as.numeric(meta_num) + 1))] # Backward ordering
+    colnames(align_pos) <- c("position", "meta")
+    align_grouped <- group_by(.data = align_pos, meta) 
+    align_tables <- as.data.frame(do(.data = align_grouped, data.frame(val = freq_pct(.[,1]))))
+    align_final <- data.frame("Position" = rep(pos_full, length(align_tables[,1])), "Meta" = align_tables[,1], "Allele" = align_tables[,2], "Freq" = align_tables[,3])
+    return(align_final)
+  }
+
+  meta_nums <- list(1, 2, 3)
+  all_tables <- lapply(meta_nums, function(x) lapply(pos, function(y) table_get(align_df, y, x)))
+  table_concat <- lapply(all_tables, function(x) base::Reduce(rbind, x))
+  return(table_concat)
+
+}
+
+umap_plotter <- function(umap_df) {
+
+  p1 <- ggplot(data = umap_df, aes(x = UMAP_1, y = UMAP_2)) +
+    theme_few() +
+    geom_jitter(aes(fill = Region), size = 3, position = "jitter", colour = "black", pch = 21, stroke = 0.25) +
+    scale_fill_manual(name = "", values = kev_palette[1:length(unique(umap_df$Region))]) +
+    labs(x = "UMAP 1", y = "UMAP 2") +
+    theme(axis.ticks.x = element_blank()) +
+    theme(axis.ticks.y = element_blank()) +
+    theme(axis.text.y = element_blank()) +
+    theme(axis.text.x = element_blank()) +
+    theme(axis.title.y = element_text(size = 16, face = "bold")) +
+    theme(axis.title.x = element_text(size = 16, face = "bold")) +
+    theme(legend.title = element_text(size = 15, face = "bold")) +
+    theme(legend.text = element_text(size = 14)) 
+
+  p2 <- ggplot(data = umap_df, aes(x = UMAP_1, y = UMAP_2)) +
+    theme_few() +
+    geom_jitter(aes(fill = Country), size = 3, position = "jitter", colour = "black", pch = 21, stroke = 0.25) +
+    scale_fill_manual(name = "", values = qual_vector[1:length(unique(umap_df$Country))]) +
+    labs(x = "UMAP 1", y = "UMAP 2") +
+    theme(axis.ticks.x = element_blank()) +
+    theme(axis.ticks.y = element_blank()) +
+    theme(axis.text.y = element_blank()) +
+    theme(axis.text.x = element_blank()) +
+    theme(axis.title.y = element_text(size = 16, face = "bold")) +
+    theme(axis.title.x = element_text(size = 16, face = "bold")) +
+    theme(legend.title = element_text(size = 15, face = "bold")) +
+    theme(legend.text = element_text(size = 14)) 
+
+  p3 <- ggplot(data = umap_df, aes(x = UMAP_1, y = UMAP_2)) +
+    theme_few() +
+    geom_jitter(aes(color = Date), size = 3, position = "jitter", alpha = 1) +
+    scale_color_gradient(name = "Days from \nfirst case", low = "#b92b27", high = "#1565C0") +
+    labs(x = "UMAP 1", y = "UMAP 2") +
+    theme(axis.ticks.x = element_blank()) +
+    theme(axis.ticks.y = element_blank()) +
+    theme(axis.text.y = element_blank()) +
+    theme(axis.text.x = element_blank()) +
+    theme(axis.title.y = element_text(size = 16, face = "bold")) +
+    theme(axis.title.x = element_text(size = 16, face = "bold")) +
+    theme(legend.title = element_text(size = 15, face = "bold")) +
+    theme(legend.text = element_text(size = 14)) 
+
+  plot_list <- list(p1, p2, p3)
+  return(plot_list)
+
+}
+
+mst_plotter <- function(mst_list, meta_df) {
+
+  graph_m1 <- mst_list[[1]]
+  graph_m2 <- mst_list[[2]]
+  graph_m3 <- mst_list[[3]]
+  lay <- mst_list[[4]]
+
+  ggnet_1 <- ggnetwork(graph_m1, layout = lay)
+  p1 <- ggplot(ggnet_1, aes(x = x, y = y, xend = xend, yend = yend)) +
+    theme_few() +
+    geom_edges(color = "gray") +
+    geom_nodes(aes(fill = Region), size = 3) +
+    scale_fill_manual(name = "", values = kev_palette[1:length(unique(meta_df$Region))]) +
+    theme(axis.title.x = element_blank()) +
+    theme(axis.title.y = element_blank()) +
+    theme(axis.text.x = element_blank()) +
+    theme(axis.text.y = element_blank()) +
+    theme(axis.ticks.x = element_blank()) +
+    theme(axis.ticks.y = element_blank()) +
+    theme(axis.line.x = element_blank()) +
+    theme(axis.line.y = element_blank()) +
+    theme(legend.title = element_text(size = 15, face = "bold")) +
+    theme(legend.text = element_text(size = 14)) 
+
+  ggnet_2 <- ggnetwork(graph_m2, layout = lay)
+  p2 <- ggplot(ggnet_2, aes(x = x, y = y, xend = xend, yend = yend)) +
+    theme_few() +
+    geom_edges(color = "gray") +
+    geom_nodes(aes(fill = Country), size = 3) +
+    scale_fill_manual(name = "", values = qual_vector[1:length(unique(meta_df$Geo_Location))]) +
+    theme(axis.title.x = element_blank()) +
+    theme(axis.title.y = element_blank()) +
+    theme(axis.text.x = element_blank()) +
+    theme(axis.text.y = element_blank()) +
+    theme(axis.ticks.x = element_blank()) +
+    theme(axis.ticks.y = element_blank()) +
+    theme(axis.line.x = element_blank()) +
+    theme(axis.line.y = element_blank()) +
+    theme(legend.title = element_text(size = 15, face = "bold")) +
+    theme(legend.text = element_text(size = 14)) 
+
+  ggnet_3 <- ggnetwork(graph_m3, layout = lay)
+  p3 <- ggplot(ggnet_3, aes(x = x, y = y, xend = xend, yend = yend)) +
+    theme_few() +
+    geom_edges(color = "gray") +
+    geom_nodes(aes(color = Date), size = 3) +
+    scale_color_continuous(name = "Days from \nfirst case", low = "#b92b27", high = "#1565C0") + 
+    theme(axis.title.x = element_blank()) +
+    theme(axis.title.y = element_blank()) +
+    theme(axis.text.x = element_blank()) +
+    theme(axis.text.y = element_blank()) +
+    theme(axis.ticks.x = element_blank()) +
+    theme(axis.ticks.y = element_blank()) +
+    theme(axis.line.x = element_blank()) +
+    theme(axis.line.y = element_blank()) +
+    theme(legend.title = element_text(size = 15, face = "bold")) +
+    theme(legend.text = element_text(size = 14)) 
+
+  plot_list <- list(p1, p2, p3)
+  return(plot_list)
+
+}
+
+snp_plotter <- function(snp_list, meta_df) {
+
+  snps_1 <- snp_list[[1]]
+  colnames(snps_1) <- c("Position", "Region", "Allele", "Freq")
+
+  snps_2 <- snp_list[[2]]
+  colnames(snps_2) <- c("Position", "Country", "Allele", "Freq")
+
+  snps_3 <- snp_list[[3]]
+  colnames(snps_3) <- c("Position", "Date", "Allele", "Freq")
+
+  p1 <- ggplot(data = snps_1, aes(x = Allele, y = Freq)) +
+    theme_few () +
+    geom_bar(stat = "identity", position = "dodge2", aes(fill = Region), color = "black") +
+    scale_fill_manual(name = "", values = kev_palette[1:length(unique(meta_df$Region))]) +
+    facet_wrap(~Position, scales = "free_x") +
+    labs(x = "Allele", y = "Frequency") + 
+    theme(axis.text.y = element_text(size = 12)) +
+    theme(axis.text.x = element_text(size = 12)) +
+    theme(axis.title.y = element_text(size = 16, face = "bold")) +
+    theme(axis.title.x = element_text(size = 16, face = "bold")) +
+    theme(legend.title = element_text(size = 15, face = "bold")) +
+    theme(legend.text = element_text(size = 14)) +
+    theme(strip.text = element_text(size = 12, face = "bold")) 
+
+  p2 <- ggplot(data = snps_2, aes(x = Allele, y = Freq)) +
+    theme_few () +
+    geom_bar(stat = "identity", position = "dodge2", aes(fill = Country), width = 1) +
+    scale_fill_manual(name = "", values = qual_vector[1:length(unique(meta_df$Geo_Location))]) +
+    facet_wrap(~Position, scales = "free") +
+    labs(x = "Allele", y = "Frequency") + 
+    theme(axis.text.y = element_text(size = 12)) +
+    theme(axis.text.x = element_text(size = 12)) +
+    theme(axis.title.y = element_text(size = 16, face = "bold")) +
+    theme(axis.title.x = element_text(size = 16, face = "bold")) +
+    theme(legend.title = element_text(size = 15, face = "bold")) +
+    theme(legend.text = element_text(size = 14)) +
+    theme(strip.text = element_text(size = 12, face = "bold"))
+
+  int_text = paste("Functionality currently not supported")
+
+  p3 <- ggplot(data = snps_3, aes(x = Allele, y = Freq)) +
+    theme_few () +
+    geom_bar(stat = "identity", position = "dodge2", aes(color = Date)) +
+    scale_color_continuous(name = "Days from \nfirst case", low = "#b92b27", high = "#1565C0") +
+    facet_wrap(~Position, scales = "free_x") +
+    labs(x = "Allele", y = "Frequency") + 
+    theme(axis.text.y = element_text(size = 12)) +
+    theme(axis.text.x = element_text(size = 12)) +
+    theme(axis.title.y = element_text(size = 16, face = "bold")) +
+    theme(axis.title.x = element_text(size = 16, face = "bold")) +
+    theme(legend.title = element_text(size = 15, face = "bold")) +
+    theme(legend.text = element_text(size = 14)) +
+    theme(strip.text = element_text(size = 12, face = "bold")) 
+
+  plot_list <- list(p1, p2, p3)
+  return(plot_list)
+
+}