figures: added workflow for manuscript figures (not finished, issue #123)

config/fig.yaml

+# working directory: will contain the results (should be writeable)
+work_dir: "/scratch/users/vgalata/ONT_pilot_manuscript"
+
+# samples: name and path to their results
+samples:
+  gdb: "/scratch/users/vgalata/gdb/results"
+  nwc: "/scratch/users/vgalata/nwc/results"
+  rumen: "/scratch/users/sbusi/rumen/results"
+  zymo: "/scratch/users/vgalata/zymo/results"
+
+# List of assemblers for different read types (same as in sample config files)
+assemblers:
+  sr: ["megahit", "metaspades"]
+  lr: ["flye", "raven"]
+  hy: ["metaspadeshybrid", "operamsmegahit", "operamsmetaspades"]
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workflow_figures/Snakefile

+# Manuscript figure pipeline: to be used after workflow/ and workflow_report/
+
+##############################
+# MODULES
+import os
+import re
+import pandas
+# from scripts.utils import assembler_pairs
+
+##############################
+# CONFIG
+
+# Paths
+SRC_DIR = srcdir("scripts")
+ENV_DIR = srcdir("envs")
+
+# default executable for snakmake
+shell.executable("bash")
+
+# working directory
+workdir:
+    config["work_dir"]
+
+##############################
+# TARGETS & RULES
+
+rule all:
+    input:
+        fig_gdb_rgi_aro3004454_flye="figures/fig_gdb_rgi_aro3004454_flye.pdf"
+
+rule fig_gdb_rgi_aro3004454_flye_metaT:
+    input:
+        os.path.join(config["samples"]["gdb"], "mapping/metat/lr/flye/ASSEMBLY.POLISHED.sr.cov.perbase")
+    output:
+        temp("figures/fig_gdb_lr_flye_contig_4930:1.0-5516.0_1-1000_metatcov.tsv")
+    shell:
+        # metaT cov. of contig contig_4930:1.0-5516.0 for bases 1-1000
+        "grep -F \"contig_4930:1.0-5516.0\" {input} | awk -F'\\t' '$1 == \"contig_4930:1.0-5516.0\" && $2 >= 1 && $2 <= 1000 {{print $0}}' > {output}"
+
+rule fig_gdb_rgi_aro3004454_flye:
+    input:
+        metat_cov=rules.fig_gdb_rgi_aro3004454_flye_metaT.output
+    output:
+        pdf="figures/fig_gdb_rgi_aro3004454_flye.pdf"
+    log:
+        "figures/fig_gdb_rgi_aro3004454_flye.log"
+    conda:
+        os.path.join(ENV_DIR, "r.yaml")
+    script:
+        os.path.join(SRC_DIR, "fig_gdb_rgi_aro3004454_flye.R")
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workflow_figures/envs/r.yaml

+../../workflow_report/envs/r.yaml
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workflow_figures/scripts/const.R

+../../workflow_report/scripts/const.R
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workflow_figures/scripts/fig_gdb_rgi_aro3004454_flye.R

+#!/usr/bin/Rscript
+
+# Figure: GDB sample, RGI results, ARO:30004454 hit in Flye assembly (LR)
+
+############################## LOG
+sink(file=file(snakemake@log[[1]], open="wt"), type=c("output", "message"))
+
+############################## LIBS
+suppressMessages(library(testit)) # assertions
+suppressMessages(library(dplyr)) # tables
+suppressMessages(library(ggplot2)) # plotting
+suppressMessages(library(ggsci)) # color palettes
+suppressMessages(library(reshape2)) # reshaping dataframes
+suppressMessages(library(scales)) # plot scales
+suppressMessages(library(viridis)) # color palettes
+
+# # custom
+# source(snakemake@params$const)
+# source(snakemake@params$utils)
+
+############################## DATA
+
+# metaT coverage: bases 1-1000 of contig contig_4930:1.0 from Flye assembly from GDB sample
+metat_cov <- read.csv(snakemake@input$metat_cov, header=FALSE, sep="\t", col.names=c("contigID", "pos", "cov"), stringsAsFactors=FALSE)
+
+# gene/protein sequences to be plotted
+seqs <- data.frame(
+    sid=c("contig_4930:1.0-5516.0_1", "ARO:30004454", "contig_4930:1.0-5516.0_1NEW"),
+    start=c(182,182,420),
+    end=c(448,806,806),
+    nucl=c(
+        "ATGCAATTCACAAAGATTGATATAAATAATTGGACACGAAAAGAGTATTTCGACCACTATTTTGACAATACGCCCTGCACATATAGTATGACGGTAAAACTCGATATTTCTAAGTTGAAAAAGGATGGAAAAAAATTATATCCGACTCTCTTATATGGGGTTACAACAATCCTCAATCGACACGAAGAGTTCAGGACGGCATTAGATAAAAACGGACAGGTAGGTGTTTTTTTCAGAAATGCTGCCTTGCTACACAATCTTTCATAA",
+        "ATGCAATTCACAAAGATTGATATAAATAATTGGACACGAAAAGAGTATTTCGACCACTATTTTGGCAATACGCCCTGCACATATAGTATGACGGTAAAACTCGATATTTCTAAGTTGAAAAAGGATGGAAAAAAGTTATACCCAACTCTTTTATATGGAGTTACAACGATCATCAATCGACATGAAGAGTTCAGGACCGCATTAGATGAAAACGGACAGGTAGGCGTTTTT-TCAGAAATGCTGCCTTGCTACACAGTTTTTCATAAGGAAACTGAAACCTTTTCGAGTATTTGGACTGAGTTTACAGCAGACTATACTGAGTTTCTTCAGAACTATCAAAAGGATATAGACGCTTTTGGTGAACGAATGGGAATGTCCGCAAAGCCTAATCCTCCGGAAAACACTTTCCCTGTTTCTATGATACCGTGGACAAGCTTTGAAGGCTTTAACTTAAATCTAAAAAAAGGATATGACTATCTACTGCCGATATTTACGTTTGGGAAGTATTATGAGGAGGGCGGAAAATACTATATTCCCTTATCGATTCAAGTGCATCATGCCGTTTGTGACGGCTTTCATGTTTGCCGTTTTTTGGATGAATTACAAGACTTGCTGAATAAATAA",
+        "ATGCTGCCTTGCTACACAATCTTTCATAAGGAAACTGAAACCTTTTCGAGTATTTGGACTGAGTTTACAGCAGACTATACTGAGTTTCTTCAGAACTATCAAAAGGATATAGACGCTTATGGTGAACGAAAGGGAATGTTCGCAAAGCCTAATCCTCCGGAAAACACTTTCCCTGTTTCTATGATACCGTGGACAAGCTTTGAAGGCTTTAACTTAAATCTAAAAAAGGGATATGACTATCTACTGCCGATATTTACGTTTGGGAAGTATTATGAGGATGGCGGAAAATACTATATTCCCTTATCGATTCAAGTGCATCATGCCGTTTGTGATGGCTTTCATGTTTGCCGTTTTTTGGATGAATTACAAGACTTGCTGAATAAATAA"
+    ),
+    prot=c(
+        "MQFTKIDINNWTRKEYFDHYFDNTPCTYSMTVKLDISKLKKDGKKLYPTLLYGVTTILNRHEEFRTALDKNGQVGVFFRNAALLHNLS*",
+        "MQFTKIDINNWTRKEYFDHYFGNTPCTYSMTVKLDISKLKKDGKKLYPTLLYGVTTIINRHEEFRTALDENGQVGVFSEMLPCYTVFHKETETFSSIWTEFTADYTEFLQNYQKDIDAFGERMGMSAKPNPPENTFPVSMIPWTSFEGFNLNLKKGYDYLLPIFTFGKYYEEGGKYYIPLSIQVHHAVCDGFHVCRFLDELQDLLNK*",
+        "MLPCYTIFHKETETFSSIWTEFTADYTEFLQNYQKDIDAYGERKGMFAKPNPPENTFPVSMIPWTSFEGFNLNLKKGYDYLLPIFTFGKYYEDGGKYYIPLSIQVHHAVCDGFHVCRFLDELQDLLNK*"
+    ),
+    stringsAsFactors=FALSE
+)
+rownames(seqs) <- seqs$sid
+
+# add seq. letters to metaT coverage
+for(sid in seqs$sid){
+    # if(sid == "ARO:30004454"){ next }
+    sid_nucl    <- unlist(strsplit(seqs[sid,"nucl"], split=""))
+    sid_prot    <- unlist(strsplit(seqs[sid,"prot"], split=""))
+    sid_start   <- seqs[sid,"start"]
+    sid_end     <- seqs[sid,"end"]
+    # print(sprintf("%s: %d, %d, %d", sid, sid_start, sid_end, length(sid_nucl)))
+    metat_cov[,sid] <- NA
+    # metat_cov[sid_start:sid_end,sid] <- sid_nucl # nucl
+    metat_cov[seq(sid_start+ifelse(sid=="contig_4930:1.0-5516.0_1NEW",0,1), sid_end, 3),sid] <- sid_prot # prot
+}
+
+# data to plot seq.s
+metat_cov_seqs <- reshape2::melt(
+    metat_cov[,setdiff(colnames(metat_cov),c("contigID", "cov"))],
+    id.vars="pos",
+    na.rm=TRUE
+)
+metat_cov_seqs$y <- as.numeric(metat_cov_seqs$variable) * -1
+
+############################## PLOT
+# custom theme
+custom_theme <-
+    theme_classic() +
+    theme(
+        panel.grid.major=element_blank(),
+        panel.grid.minor=element_blank(),
+        legend.position="none"
+    )
+
+# AA colors
+aa_colors <- c(pal_d3(palette="category20")(20), "black")
+names(aa_colors) <- c(setdiff(sort(unique(metat_cov_seqs$value)), "*"),"*")
+
+# Nucl. colors
+# nc_colors <- c(pal_d3(palette="category20")(4), "black")
+# names(nc_colors) <- c("A", "T", "C", "G", "-")
+
+# Plot
+p_cov  <-
+    ggplot(data=metat_cov %>% filter(pos >= 160, pos <= 830), aes(x=pos, y=cov)) +
+    # overlap area
+    geom_polygon(data=data.frame(x=c(182+238+29,182+238,182+238,182+238+29), y=c(-6,-6,30,30)), aes(x=x, y=y), fill="gray", alpha=0.3) +
+    # cov. baseline
+    geom_hline(yintercept=0, linetype="dotted") +
+    # cov.
+    geom_step() +
+    # seq.s
+    geom_label(
+        data=metat_cov_seqs,
+        aes(y=y, label=value, fill=value),
+        color="white", size=2, fontface="bold",
+        label.padding=unit(0.1, "lines"), label.size=0, label.r=unit(0, "lines")
+    ) +
+    # seq. annotations
+    annotate(
+        geom="segment",
+        x=c(182, 182, 404), y=c(1.5, -4.5, -4.5),
+        xend=c(182, 182, 417), yend=c(-0.5, -2.5, -3), 
+        arrow=arrow(length=unit(2, "mm"))
+    ) +
+    annotate(
+        geom="text",
+        x=c(182, 182, 402), y=c(2, -5, -5),
+        label=levels(metat_cov_seqs$variable),
+        hjust=c("left", "left", "right"),
+        size=4
+    ) +
+    # colors
+    scale_fill_manual(values=aa_colors) +
+    # axis range
+    scale_x_continuous(limits=c(160, 830), expand=c(0, 0)) +
+    scale_y_continuous(limits=c(-6,30), expand=c(0, 0)) +
+    # titles
+    labs(
+        x="Contig position (LR, Flye, contig_4930:1.0-5516.0)",
+        y="metaT coverage"
+    ) +
+    # theme
+    custom_theme
+
+# PDF
+pdf(snakemake@output$pdf, width=20, height=5)
+print(p_cov)
+dev.off()
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workflow_figures/scripts/utils.R

+../../workflow_report/scripts/utils.R
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workflow_figures/scripts/utils.py

+../../workflow/scripts/utils.py
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