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umap_list.R
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umap_list.R
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#' UMAP Projection
#'
#' @author Steven P. Sanderson II, MPH
#'
#' @description Create a umap object from the [uwot::umap()] function.
#'
#' @seealso
#' * \url{https://cran.r-project.org/package=uwot} (CRAN)
#' * \url{https://github.com/jlmelville/uwot} (GitHub)
#' * \url{https://github.com/jlmelville/uwot} (arXiv paper)
#'
#' @details This takes in the user item table/matix that is produced by [kmeans_user_item_tbl()]
#' function. This function uses the defaults of [uwot::umap()].
#'
#' @param .data The data from the [kmeans_user_item_tbl()] function.
#' @param .kmeans_map_tbl The data from the [kmeans_mapped_tbl()].
#' @param .k_cluster Pick the desired amount of clusters from your analysis of the scree plot.
#'
#' @examples
#' library(healthyR.data)
#' library(healthyR)
#' library(dplyr)
#' library(broom)
#'
#' data_tbl <- healthyR_data %>%
#' filter(ip_op_flag == "I") %>%
#' filter(payer_grouping != "Medicare B") %>%
#' filter(payer_grouping != "?") %>%
#' select(service_line, payer_grouping) %>%
#' mutate(record = 1) %>%
#' as_tibble()
#'
#' uit_tbl <- kmeans_user_item_tbl(
#' .data = data_tbl
#' , .row_input = service_line
#' , .col_input = payer_grouping
#' , .record_input = record
#' )
#'
#' kmm_tbl <- kmeans_mapped_tbl(uit_tbl)
#'
#' umap_list(.data = uit_tbl, kmm_tbl, 3)
#'
#' @return A list of tibbles and the umap object
#'
#' @export
#'
umap_list <- function(.data
, .kmeans_map_tbl
, .k_cluster = 5) {
# * Tidyeval ----
k_cluster_var_expr <- .k_cluster
# * Checks ----
if (!is.data.frame(.data)) {
stop(call. = FALSE,
"(.data) is not a data.frame/tibble. Please supply.")
}
if (!is.data.frame(.kmeans_map_tbl)) {
stop(call. = FALSE,
"(.kmeans_map_tbl) is not a data.frame/tibble. Please supply.")
}
# * Data ----
data <- tibble::as_tibble(.data)
kmeans_map_tbl <- tibble::as_tibble(.kmeans_map_tbl)
# * Manipulation ----
umap_obj <- data %>%
dplyr::select(-1) %>%
uwot::umap()
umap_results_tbl <- umap_obj %>%
tibble::as_tibble() %>%
purrr::set_names("x", "y") %>%
dplyr::bind_cols(data %>% dplyr::select(1))
kmeans_obj <- kmeans_map_tbl %>%
dplyr::pull(k_means) %>%
purrr::pluck(k_cluster_var_expr)
kmeans_cluster_tbl <- kmeans_obj %>%
broom::augment(data) %>%
dplyr::select(1, .cluster)
umap_kmeans_cluster_results_tbl <- umap_results_tbl %>%
dplyr::left_join(kmeans_cluster_tbl)
# * Data List ----
list_names <-
df_list <- list(
umap_obj = umap_obj,
umap_results_tbl = umap_results_tbl,
kmeans_obj = kmeans_obj,
kmeans_cluster_tbl = kmeans_cluster_tbl,
umap_kmeans_cluster_results_tbl = umap_kmeans_cluster_results_tbl
)
# * Return ----
return(df_list)
}
#' UMAP and K-Means Cluster Visualization
#'
#' @author Steven P. Sanderson II, MPH
#'
#' @description Create a UMAP Projection plot.
#'
#' @seealso
#' * \url{https://cran.r-project.org/package=uwot} (CRAN)
#' * \url{https://github.com/jlmelville/uwot} (GitHub)
#' * \url{https://github.com/jlmelville/uwot} (arXiv paper)
#'
#' @details This takes in `umap_kmeans_cluster_results_tbl` from the [umap_list()]
#' function output.
#'
#' @param .data The data from the [umap_list()] function.
#' @param .point_size The desired size for the points of the plot.
#' @param .label Should [ggrepel::geom_label_repel()] be used to display cluster
#' user labels.
#'
#' @examples
#' library(healthyR.data)
#' library(healthyR)
#' library(dplyr)
#' library(broom)
#' library(ggplot2)
#'
#' data_tbl <- healthyR_data %>%
#' filter(ip_op_flag == "I") %>%
#' filter(payer_grouping != "Medicare B") %>%
#' filter(payer_grouping != "?") %>%
#' select(service_line, payer_grouping) %>%
#' mutate(record = 1) %>%
#' as_tibble()
#'
#' uit_tbl <- kmeans_user_item_tbl(
#' .data = data_tbl
#' , .row_input = service_line
#' , .col_input = payer_grouping
#' , .record_input = record
#' )
#'
#' kmm_tbl <- kmeans_mapped_tbl(uit_tbl)
#'
#' ump_lst <- umap_list(.data = uit_tbl, kmm_tbl, 3)
#'
#' umap_plt(.data = ump_lst, .point_size = 3)
#'
#' @return A ggplot2 UMAP Projection with clusters represented by colors.
#'
#' @export
#'
umap_plt <- function(.data, .point_size = 2, .label = TRUE) {
# * Checks ----
if(!is.list(.data)){
stop(call. = FALSE,"(.data) is not a list")
}
# * Data ----
ump_lst <- .data
ump_tbl <- ump_lst$umap_kmeans_cluster_results_tbl
optimal_k <- max(ump_lst$kmeans_obj$cluster)
umap_plt <- ump_tbl %>%
ggplot2::ggplot(
mapping = ggplot2::aes(
x = x
, y = y
)
) +
ggplot2::geom_point(size = .point_size, ggplot2::aes(col = .cluster)) +
ggplot2::theme_minimal()
ggplot2::labs(
subtitle = "UMAP 2D Projection with K-Means Cluster Assignment"
, caption = stringr::str_c(
"Conclusion:"
, optimal_k
, "Clusters Identified"
, sep = " "
)
, color = "Cluster"
)
if(.label){
ump_label <- ump_lst$umap_kmeans_cluster_results_tbl[[3]]
umap_plt <- umap_plt +
ggrepel::geom_label_repel(
mapping = ggplot2::aes(
label = ump_label
)
)
}
# * Return ----
print(umap_plt)
}