comparison dose_response.R @ 1:8a1b524ed9d8 draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit dca5f947ae4c9697ac0cfce0b313170b541124e5

0:082e9d22c38d

        theme(
            panel.background = element_rect(fill = "white", color = NA),
            plot.background = element_rect(fill = "white", color = NA)
        )

    ggsave(filename = plot_file, plot = p, device = "jpg")
}

dose_response_analysis <- function(data, concentration_col, response_col, plot_file, ec_file) {
    models <- fit_models(data, concentration_col, response_col)
    best_model_info <- select_best_model(models)
    ec_values <- calculate_ec_values(best_model_info$model)
    plot_dose_response(best_model_info$model, data, ec_values, concentration_col, response_col, plot_file)

    ec_data <- data.frame(
        EC10 = ec_values$EC10[1],
        EC25 = ec_values$EC25[1],
        EC50 = ec_values$EC50[1]
    )
    write.csv(ec_data, ec_file, row.names = FALSE)

    return(list(best_model = best_model_info$name, ec_values = ec_values))
}

args <- commandArgs(trailingOnly = TRUE)

concentration_col <- args[2]
response_col <- args[3]
plot_file <- args[4]
ec_file <- args[5]

data <- read.csv(data_file, header = TRUE)
dose_response_analysis(data, concentration_col, response_col, plot_file, ec_file)

1:8a1b524ed9d8

        theme(
            panel.background = element_rect(fill = "white", color = NA),
            plot.background = element_rect(fill = "white", color = NA)
        )

    jpeg(filename = plot_file)
    print(p)
    dev.off()
}

dose_response_analysis <- function(data, concentration_col, response_col, plot_file, ec_file) {
    concentration_col <- colnames(data)[as.integer(concentration_col)]
    response_col <- colnames(data)[as.integer(response_col)]
    models <- fit_models(data, concentration_col, response_col)
    best_model_info <- select_best_model(models)
    ec_values <- calculate_ec_values(best_model_info$model)
    plot_dose_response(best_model_info$model, data, ec_values, concentration_col, response_col, plot_file)

    ec_data <- data.frame(
        EC10 = ec_values$EC10[1],
        EC25 = ec_values$EC25[1],
        EC50 = ec_values$EC50[1]
    )
    write.table(ec_data, ec_file, sep = "\t", row.names = FALSE, col.names = TRUE, quote = FALSE)

    return(list(best_model = best_model_info$name, ec_values = ec_values))
}

args <- commandArgs(trailingOnly = TRUE)

concentration_col <- args[2]
response_col <- args[3]
plot_file <- args[4]
ec_file <- args[5]

data <- read.csv(data_file, header = TRUE, sep = "\t")
dose_response_analysis(data, concentration_col, response_col, plot_file, ec_file)