Commit fd335a85 authored by arsenij.ustjanzew's avatar arsenij.ustjanzew
Browse files

cluster_characterization() method with validation

parent cce9cfdb
#' Renders a barplot for cluster characterization
#'
#' @param object A \linkS4class{i2dash::i2dashboard} object.
#' @param cluster Values for the membership to clusters. In case of a nested list, a dropdown menu will be provided in the interactive mode.
#' @param x Numeric values mapped to the x-axis. In case of a nested list, a dropdown menu will be provided in the interactive mode. If x is NULL then a barplot for "Number of cells" per cluster will be created. If x is not NULL a barplot for "Fraction per cell" per cluster will be created.
#' @param title A title that will be displayed on top.
#'
#' @return A string containing markdown code for the rendered textbox
cluster_characterization_barplot <- function(object, x, cluster, title = "Characterization of clusters") {
# Create random env id
env_id <- paste0("env_", stringi::stri_rand_strings(1, 6, pattern = "[A-Za-z0-9]"))
# validate input, create environment variables, save environment object
.validate_input_cluster_characterizatio_barplot(object@workdir, env_id, x, cluster)
timestamp <- Sys.time()
expanded_component <- knitr::knit_expand(file = system.file("templates", "cluster_characterization_barplot_template.Rmd", package = "i2dash.scrnaseq"), title = title, env_id = env_id, date = timestamp)
return(expanded_component)
}
.validate_input_cluster_characterizatio_barplot <- function(workdir, env_id, x, cluster) {
env <- new.env()
env$x_selection <- FALSE
env$cluster_selection <- FALSE
# Check existence of cluster
if(is.null(cluster)) stop("cluster is required.")
# Create lists if needed
if(!is.list(x) & !is.null(x)) x <- list(x)
if(!is.list(cluster)) cluster <- list(cluster)
# should I use magrittr::%<>% ?
# name the lists
library(magrittr)
if(is.null(names(cluster))) x %<>% magrittr::set_names("clustering.1")
if(is.null(names(x)) & !is.null(x)) x %<>% magrittr::set_names("x")
# Check validity
if(!all(sapply(cluster, is.factor))) stop("'cluster' should only contain factorial values.")
if(!all(sapply(x, is.factor))) stop("'x' should only contain factorial values.")
# Check if lengths in a list are the same and if x and y and label and color_by are the same length
#if(length(unique(sapply(x, length))) != 1) stop("list x should contain elements with the same length.")
#if(length(unique(sapply(y, length))) != 1) stop("list y should contain elements with the same length.")
#if(!identical(length(x[[1]]), length(y[[1]]))) stop("all arguments should be of the the same length.")
#if(!identical(length(x[[1]]), length(colour_by[[1]])) & !is.null(colour_by)) stop("all arguments should be of the the same length.")
#if(!identical(length(x[[1]]), length(labels[[1]])) & !is.null(labels)) stop("all arguments should be of the the same length.")
# Add objects to env
env$x <- x
env$x_selection <- length(env$x) > 1
env$cluster <- cluster
env$cluster_selection <- length(env$cluster) > 1
# save environment as rds-object
saveRDS(env, file = file.path(workdir, "envs", paste0(env_id, ".rds")))
print("validation TRUE")
}
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