forked from mj163163/ggcor
-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
9 changed files
with
724 additions
and
3 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,197 @@ | ||
| #' 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))) | ||
| } |
Oops, something went wrong.