ENHANCED VOLCANO

Build Volcano-plots with EnhancedVolcano

URL: https://bioconductor.org/packages/3.17/bioc/html/EnhancedVolcano.html

Example

This wrapper can be used in the following way:

rule test_enhanced_volcano_tsv:
    input:
        "table.tsv",
    output:
        "volcano_tsv.png",
    threads: 1
    log:
        "logs/enhanced-volcano/tsv.log",
    params:
        extra="lab='Gene_id', x='ShrinkedFC', y='adjusted_pvalues'",
        width=1024,  # Optional PNG width
        height=768,  # Optional PNG height
    wrapper:
        "v3.9.0/bio/enhancedvolcano"


rule test_enhanced_volcano_csv:
    input:
        "table.csv",
    output:
        "volcano_csv.svg",
    threads: 1
    log:
        "logs/enhanced-volcano/csv.log",
    params:
        extra="lab='Gene_id', x='ShrinkedFC', y='adjusted_pvalues'",
        # width=7,  # Optional PNG width
        # height=7,  # Optional PNG height
    wrapper:
        "v3.9.0/bio/enhancedvolcano"


rule test_enhanced_volcano_rds:
    input:
        "table.RDS",
    output:
        "volcano_rds.svg",
    threads: 1
    log:
        "logs/enhanced-volcano/rds.log",
    params:
        extra="lab='Gene_id', x='ShrinkedFC', y='adjusted_pvalues'",
        # width=7,  # Optional PNG width
        # height=7,  # Optional PNG height
    wrapper:
        "v3.9.0/bio/enhancedvolcano"

Note that input, output and log file paths can be chosen freely.

When running with

snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.

Notes

• Input table requires at least the following: column for variable names; a column for log2 fold changes; a column for nominal or adjusted p-value.

Software dependencies

• bioconductor-enhancedvolcano=1.20.0

Input/Output

Input:

• Path to a TSV/CSV table (separator are inferred from file extension) or a RDS formatted object convertible into a data.frame.

Output:

• Path to SVG or PNG formatted Volcano plot

Params

• extra: additional parameters besides toptable

• height: plot default height (in grDevices::svg)

• width: plot default width (in grDevices::svg)

Authors

• Thibault Dayris

Code

# __author__ = "Thibault Dayris"
# __copyright__ = "Copyright 2023, Thibault Dayris"
# __email__ = "thibault.dayris@gustaveroussy.fr"
# __license__ = "MIT"

# This script builds a Volcano plot from a table or
# a RDS object that can be casted into a data.frame

# Sink the stderr and stdout to the snakemake log file
# https://stackoverflow.com/a/48173272
log.file <- base::file(snakemake@log[[1]], open = "wt")
base::sink(log.file)
base::sink(log.file, type = "message")

# Loading Libraries and input data
base::library(package = "EnhancedVolcano", character.only = TRUE)
base::message("Library loaded")

save_png <- function(output_path, width, height) {
  grDevices::png(
    filename = output_path,
    width = width,
    height = height,
  )

  base::print(base::eval(base::parse(text = cmd)))

  grDevices::dev.off()
}

save_svg <- function(output_path, width, height) {
  grDevices::svg(
    filename = output_path,
    width = width,
    height = height
  )

  base::print(base::eval(base::parse(text = cmd)))

  grDevices::dev.off()
}

input_path <- base::as.character(x = snakemake@input[[1]])
toptable <- NULL
if (base::endsWith(x = input_path, suffix = ".tsv")) {
  toptable <- utils::read.table(
    file = input_path,
    header = TRUE,
    sep = "\t",
    stringsAsFactors = FALSE,
  )
} else if (base::endsWith(x = input_path, suffix = ".csv")) {
  toptable <- utils::read.table(
    file = input_path,
    header = TRUE,
    sep = ",",
    stringsAsFactors = FALSE,
  )
} else if (base::endsWith(x = input_path, suffix = ".RDS")) {
  toptable <- base::readRDS(file = input_path)
} else {
  base::stop(
    "Input file format unknown. Expected either '.tsv', '.csv', or 'RDS'"
  )
}
base::message("Data loaded")
base::print(toptable)

# Building command line
extra <- "toptable = toptable"
if ("extra" %in% base::names(snakemake@params)) {
  extra <- base::paste(
    extra,
    base::as.character(x = snakemake@params[["extra"]]),
    sep = ","
  )
}

width <- 7
if ("width" %in% base::names(snakemake@params)) {
  width <- base::as.numeric(x = snakemake@params[["width"]])
}
height <- 7
if ("height" %in% base::names(snakemake@params)) {
  height <- base::as.numeric(x = snakemake@params[["height"]])
}


cmd <- base::paste0(
  "EnhancedVolcano::EnhancedVolcano(",
  extra,
  ")"
)
base::message("Command line: ")
base::message(cmd)


# Run EnhancedVolcano
outfile <- base::as.character(x = snakemake@output[[1]])
if (base::endsWith(x = outfile, suffix = ".png")) {
  save_png(output_path = outfile, width = width, height = height)
} else {
  save_svg(output_path = outfile, width = width, height = height)
}
base::message("Process over")

# Proper syntax to close the connection for the log file
# but could be optional for Snakemake wrapper
base::sink(type = "message")
base::sink()