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| #' Transform data | ||
| #' @description These layout functions are not layout in the network diagram, | ||
| #' it just converts the original data into a form that makes it easy to draw | ||
| #' a curve graph. | ||
| #' @param data a data frame. | ||
| #' @param start.var,end.var character to specify which variable is the starting | ||
| #' points and which is the ending points. if the variable is not character, it | ||
| #' is forced to be converted. | ||
| #' @param horiz a logical value. If FALSE, the parallel graph are drawn vertically. | ||
| #' If TRUE, the parallel graph are drawn horizontally. | ||
| #' @param sort.start,sort.end charater vector, the nodes will be sorted by this parameter. | ||
| #' @param start.x,start.y,end.x,end.y numeric to specify the x (horiz = TRUE) or y | ||
| #' (horiz = FALSE) coordinates. | ||
| #' @param type the type (""upper" or "lower") of the correlation matrix plot. | ||
| #' @param show.diag a logical value indicating whether keep the diagonal. | ||
| #' @param row.names,col.names row/column names of correlation matrix. | ||
| #' @param cor_tbl a col_tbl object. | ||
| #' @return a data frame. | ||
| #' @importFrom rlang enquo eval_tidy set_names quo_is_null | ||
| #' @importFrom dplyr filter | ||
| #' @rdname create-layout | ||
| #' @examples | ||
| #' cor_tbl(cor(mtcars)) %>% | ||
| #' parallel_layout() | ||
| #' \dontrun{ | ||
| #' data("varespec", package = "vegan") | ||
| #' data("varechem", package = "vegan") | ||
| #' mantel_test(varespec, varechem) %>% | ||
| #' combination_layout(type = "upper", col.names = colnames(varechem), | ||
| #' show.diag = FALSE) | ||
| #' } | ||
| #' @author Houyun Huang, Lei Zhou, Jian Chen, Taiyun Wei | ||
| #' @export | ||
| parallel_layout <- function(data, | ||
| start.var = NULL, | ||
| end.var = NULL, | ||
| horiz = FALSE, | ||
| sort.start = NULL, | ||
| sort.end = NULL, | ||
| start.x = NULL, | ||
| start.y = NULL, | ||
| end.x = NULL, | ||
| end.y = NULL) | ||
| { | ||
| if(!is.data.frame(data)) | ||
| data <- as.data.frame(data) | ||
| start <- if(rlang::quo_is_null(enquo(start.var))) { | ||
| data[[1]] | ||
| } else { | ||
| rlang::eval_tidy(rlang::enquo(start.var), data) | ||
| } | ||
| end <- if(rlang::quo_is_null(enquo(end.var))) { | ||
| data[[2]] | ||
| } else { | ||
| rlang::eval_tidy(rlang::enquo(end.var), data) | ||
| } | ||
| if(!is.character(start)) | ||
| start <- as.character(start) | ||
| if(!is.character(end)) | ||
| end <- as.character(end) | ||
|
|
||
| unique.start <- unique(start[!is.na(start)]) | ||
| unique.end <- unique(end[!is.na(end)]) | ||
| n <- max(length(unique.start), length(unique.end)) | ||
| if(!is.null(sort.start) && length(sort.start) != length(unique.start)) { | ||
| stop("Length of 'sort.start' and unique elements of 'start' don't match.", | ||
| call. = FALSE) | ||
| } | ||
| if(!is.null(sort.end) && length(sort.end) != length(unique.end)) { | ||
| stop("Length of 'sort.end' and unique elements of 'end' don't match.", | ||
| call. = FALSE) | ||
| } | ||
| start.pos <- if(is.null(sort.start)) { | ||
| rlang::set_names(seq(1, n, length.out = length(unique.start)), unique.start) | ||
| } else { | ||
| rlang::set_names(seq_len(length.out = length(sort.start)), sort.start) | ||
| } | ||
| end.pos <- if(is.null(sort.start)) { | ||
| rlang::set_names(seq(1, n, length.out = length(unique.end)), unique.end) | ||
| } else { | ||
| rlang::set_names(seq_len(length.out = length(sort.end)), sort.end) | ||
| } | ||
| pos <- if(horiz) { | ||
| tibble::tibble(x = start.pos[start], y = start.y %||% 0, xend = end.pos[end], | ||
| start.label = start, end.label = end, yend = end.y %||% 1, | ||
| .start.filter = !duplicated(start) & !is.na(start), | ||
| .end.filter = !duplicated(end) & !is.na(end)) | ||
| } else { | ||
| tibble::tibble(x = start.x %||% 0, y = start.pos[start], xend = end.x %||% 1, | ||
| start.label = start, end.label = end, yend = end.pos[end], | ||
| .start.filter = !duplicated(start) & !is.na(start), | ||
| .end.filter = !duplicated(end) & !is.na(end)) | ||
| } | ||
| structure(.Data = dplyr::bind_cols(pos, data), | ||
| class = c("layout_link_tbl", class(pos))) | ||
| } | ||
|
|
||
| #' @rdname create-layout | ||
| #' @export | ||
| combination_layout <- function(data, | ||
| type = NULL, | ||
| show.diag = NULL, | ||
| row.names = NULL, | ||
| col.names = NULL, | ||
| start.var = NULL, | ||
| end.var = NULL, | ||
| cor_tbl) | ||
| { | ||
| non.cor.tbl <- missing(cor_tbl) | ||
| if(!non.cor.tbl) { | ||
| if(!is_cor_tbl(cor_tbl) || !is_symmet(cor_tbl)) | ||
| stop("Need a symmetric cor_tbl.", call. = FALSE) | ||
| } | ||
| row.names <- if(non.cor.tbl) { | ||
| rev(row.names) %||% col.names | ||
| } else { | ||
| rev(get_row_name(cor_tbl)) | ||
| } | ||
| type <- if(non.cor.tbl) type else get_type(cor_tbl) | ||
| show.diag <- if(non.cor.tbl) show.diag else get_show_diag(cor_tbl) | ||
| start <- if(rlang::quo_is_null(enquo(start.var))) { | ||
| data[[1]] | ||
| } else { | ||
| rlang::eval_tidy(rlang::enquo(start.var), data) | ||
| } | ||
| end <- if(rlang::quo_is_null(enquo(end.var))) { | ||
| data[[2]] | ||
| } else { | ||
| rlang::eval_tidy(rlang::enquo(end.var), data) | ||
| } | ||
| if(!is.character(start)) | ||
| start <- as.character(start) | ||
| if(!is.character(end)) | ||
| end <- as.character(end) | ||
|
|
||
| spec.name <- unique(start[!is.na(start)]) | ||
| n <- length(row.names) | ||
| m <- length(spec.name) | ||
| ## get position of spec point | ||
| if(type == "full") { | ||
| stop("The 'type' of cor_tbl is not supported.", call. = FALSE) | ||
| } | ||
|
|
||
| if(type == "upper") { | ||
| if(m == 1) { | ||
| x <- 0.5 + 0.18 * n | ||
| y <- 0.5 + 0.3 * n | ||
| } else if(m == 2) { | ||
| x <- c(0.5 - 0.02 * n, 0.5 + 0.2 * n) | ||
| y <- c(0.5 + 0.46 * n, 0.5 + 0.2 * n) | ||
| } else { | ||
| y <- seq(0.5 + n * (1 - 0.3), 0.5 + n * 0.1, length.out = m) | ||
| x <- seq(0.5 - 0.25 * n, 0.5 + 0.3 * n, length.out = m) | ||
| } | ||
| } else if(type == "lower") { | ||
| if(m == 1) { | ||
| x <- 0.5 + 0.82 * n | ||
| y <- 0.5 + 0.7 * n | ||
| } else if(m == 2) { | ||
| x <- c(0.5 + 0.8 * n, 0.5 + 1.02 * n) | ||
| y <- c(0.5 + 0.8 * n, 0.5 + 0.54 * n) | ||
| } else { | ||
| y <- seq(0.5 + n * (1 - 0.1), 0.5 + n * 0.3, length.out = m) | ||
| x <- seq(0.5 + 0.75 * n, 0.5 + 1.3 * n, length.out = m) | ||
| } | ||
| } | ||
| x <- rlang::set_names(x, spec.name) | ||
| y <- rlang::set_names(y, spec.name) | ||
|
|
||
| ## get position of env point | ||
| xend <- n:1 | ||
| yend <- 1:n | ||
| if(type == "upper") { | ||
| if(show.diag) { | ||
| xend <- xend - 2 | ||
| } else { | ||
| xend <- xend - 1 | ||
| } | ||
| } else { | ||
| if(show.diag) { | ||
| xend <- xend + 2 | ||
| } else { | ||
| xend <- xend + 1 | ||
| } | ||
| } | ||
| xend <- rlang::set_names(xend, row.names) | ||
| yend <- rlang::set_names(yend, row.names) | ||
|
|
||
| ## bind postion end data | ||
| pos <- tibble::tibble(x = x[start], y = y[start], | ||
| xend = xend[end], yend = yend[end], | ||
| start.label = start, end.label = end, | ||
| .start.filter = !duplicated(start) & !is.na(start), | ||
| .end.filter = !duplicated(end) & !is.na(end)) | ||
| structure(.Data = dplyr::bind_cols(pos, data), | ||
| class = c("layout_link_tbl", class(pos))) | ||
| } |
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