R/classyfire.R

In tidymass/tinytools: All the usefull tools for MS data processing and analysis

#' @title get_compound_class
#' @description Get the class information of a compound using classyfire.
#' @author Xiaotao Shen
#' \email{shenxt1990@@outlook.com}
#' @param inchikey The inchikey ID of a metabolite.
#' @param server server.
#' @param sleep Sleep time for system. Second.
#' @return A classyfire class object.
#' @export
#' @examples
#' get_compound_class()
get_compound_class <-
    function(inchikey = "QZDWODWEESGPLC-UHFFFAOYSA-N",
             server = "http://classyfire.wishartlab.com/entities/",
             sleep = 5) {
        url <- paste(server, inchikey, sep = "")
        Sys.sleep(time = sleep)
        result <- try(expr = xml2::read_html(url), silent = TRUE)
        if (class(result)[1] == "try-error") {
            message(crayon::red(
                clisymbols::symbol$cross, inchikey,
                "is not available in website.\nPlease check this link:\n", 
                url, "\n"
            ))
            return(NA)
        }
        result <-
            try(result %>% rvest::html_nodes(css = ".main_card"), silent = TRUE)

        if (class(result)[1] == "try-error") {
            message(crayon::red(
                clisymbols::symbol$cross, inchikey,
                "is not available in website.\nPlease check this link:\n",
                url, "\n"
            ))
            return(NA)
        }
        result <- try(rvest::html_text(x = result, trim = TRUE))
        if (class(result)[1] == "try-error") {
            message(crayon::red(
                clisymbols::symbol$cross, inchikey,
                "is not available in website.\nPlease check this link:\n",
                url, "\n"
            ))
            return(NA)
        }

        compound_info <-
            try(result[[1]] %>%
                stringr::str_replace_all("\n", "{}") %>%
                stringr::str_split("\\{\\}") %>% `[[`(1) %>%
                stringr::str_trim(side = "both") %>%
                tibble::enframe(name = NULL) %>%
                dplyr::filter(value != "") %>% dplyr::pull(value) %>%
                lapply(function(x) {
                    if (x %in% c("SMILES", "InChIKey", "Formula", "Mass")) {
                        tibble::tibble(name = x, value = .[which(x == .) + 1])
                    }
                }) %>% do.call(rbind, .) %>% tibble::as_tibble() %>%
                dplyr::distinct(name, value), silent = TRUE)
        classification_info <-
            try(result[[2]] %>%
                stringr::str_replace_all("\n", "{}") %>%
                stringr::str_split("\\{\\}") %>% `[[`(1) %>%
                stringr::str_trim(side = "both") %>%
                tibble::enframe(name = NULL) %>% dplyr::filter(value != "") %>%
                dplyr::filter(!value %in% c(
                    "Taxonomic Classification",
                    "Taxonomy Tree"
                )) %>%
                dplyr::pull(value), silent = TRUE)
        idx <- try(classification_info %>% `==`("Kingdom") %>% which())
        taxonomy_tree <-
            try(classification_info[idx[1]:(idx[2] - 1)] %>%
                matrix(ncol = 2, byrow = TRUE) %>%
                tibble::as_tibble(.name_repair = "minimal"))
        try(colnames(taxonomy_tree) <- c("name", "value"))
        if (class(taxonomy_tree)[1] == "try-error") {
            taxonomy_tree <- tibble::tibble(name = c(
                "Kingdom", "Superclass",
                "Class", "Subclass"
            ), value = rep(NA, 4))
            message(crayon::red(
                clisymbols::symbol$cross, inchikey,
                "is not available in website.\n"
            ))
        } else {
            message(crayon::green(
                clisymbols::symbol$tick,
                inchikey, "is available in website.\n"
            ))
        }
        classification_info <-
            try(result[[2]] %>%
                stringr::str_replace_all("\n", "{}") %>%
                stringr::str_split("\\{\\}") %>% `[[`(1) %>%
                stringr::str_trim(side = "both") %>%
                tibble::enframe(name = NULL) %>%
                dplyr::filter(value != "") %>% dplyr::pull(value) %>%
                lapply(function(x) {
                    if (x %in% c(
                        "Kingdom", "Superclass", "Class", "Subclass",
                        "Intermediate Tree Nodes", "Direct Parent",
                        "Alternative Parents",
                        "Molecular Framework", "Substituents"
                    )) {
                        tibble::tibble(name = x, value = .[which(x == .) + 1])
                    }
                }) %>% do.call(rbind, .) %>% tibble::as_tibble() %>%
                dplyr::distinct(name, value), silent = TRUE)
        description <-
            try(result[[3]] %>% stringr::str_replace_all("\n", "{}") %>%
                stringr::str_split("\\{\\}") %>% `[[`(1) %>%
                stringr::str_trim(side = "both") %>% 
                    tibble::enframe(name = NULL) %>%
                dplyr::filter(value != "") %>%
                dplyr::pull(value) %>%
                lapply(function(x) {
                    if (x %in% c("Description")) {
                        tibble::tibble(name = x, value = .[which(x == .) + 1])
                    }
                }) %>%
                do.call(rbind, .) %>% tibble::as_tibble() %>%
                dplyr::distinct(name, value), silent = TRUE)
        external_descriptors <-
            try(result[[4]] %>%
                stringr::str_replace_all("\n", "{}") %>%
                stringr::str_split("\\{\\}") %>% `[[`(1) %>%
                stringr::str_trim(side = "both") %>%
                tibble::enframe(name = NULL) %>%
                dplyr::filter(value != "") %>% dplyr::pull(value) %>%
                lapply(function(x) {
                    if (x %in% c("External Descriptors")) {
                        tibble::tibble(name = x, value = .[which(x == .) + 1])
                    }
                }) %>%
                do.call(rbind, .) %>% tibble::as_tibble() %>%
                dplyr::distinct(name, value), silent = TRUE)
        if (class(compound_info)[1] == "try-error") {
            compound_info <-
                tibble::tibble(
                    name = c("SMILES", "InChIKey", "Formula", "Mass"),
                    value = rep(NA, 4)
                )
        }
        if (class(classification_info)[1] == "try-error") {
            classification_info <-
                tibble::tibble(
                    name = c(
                        "Kingdom", "Superclass", "Class", "Subclass",
                        "Intermediate Tree Nodes", "Direct Parent", 
                        "Alternative Parents",
                        "Molecular Framework", "Substituents"
                    ),
                    value = rep(NA, 9)
                )
        }
        if (class(description)[1] == "try-error") {
            description <- tibble::tibble(
                name = "Description",
                value = NA
            )
        }
        if (class(external_descriptors)[1] == "try-error") {
            external_descriptors <- tibble::tibble(
                name = "External Descriptors",
                value = NA
            )
        }
        result <- new(Class = "classyfire")
        result@compound_info <- compound_info
        result@taxonomy_tree <- taxonomy_tree
        result@classification_info <- classification_info
        result@description <- description
        result@external_descriptors <- external_descriptors
        return(result)
    }


setClass(
    Class = "classyfire",
    representation = representation(
        compound_info = "tbl_df",
        taxonomy_tree = "tbl_df",
        classification_info = "tbl_df",
        description = "tbl_df",
        external_descriptors = "tbl_df"
    )
)


setMethod("show",
    signature = "classyfire",
    function(object) {
        cat(cli::rule(
            left = crayon::bold("classyfire Object"),
            right = paste0("metflow2 v", utils::packageVersion("metflow2"))
        ), "\n")

        cat(crayon::red(
            "Object Size:",
            format(utils::object.size(object), units = "Kb"),
            "\n",
            "\n"
        ))

        cat(crayon::green("Information:"), "\n")

        cat(
            "SMILES: ",
            dplyr::pull(object@compound_info, "value")[1],
            "\n"
        )
        cat(
            "InChIKey: ",
            dplyr::pull(object@compound_info, "value")[2],
            "\n"
        )
        cat(
            "Formula: ",
            dplyr::pull(object@compound_info, "value")[3],
            "\n"
        )
        cat("Mass: ", dplyr::pull(object@compound_info, "value")[4], "\n")


        tree_list <-
            object@taxonomy_tree

        tree_df <- data.frame(
            stringsAsFactors = FALSE,
            id = tree_list$name,
            connections = I(c(
                as.list(tree_list$name)[-1], list(character(0))
            ))
        )

        tree_df$label <-
            paste0(
                crayon::bold(tree_df$id),
                " : ",
                cli::col_cyan(tree_list$value)
            )

        print(cli::tree(tree_df))
    }
)