R/directions.R

In epurdom/clusterExperimentShiny: A Shiny App to accompany clusterExperiment

#################
##Description####
#This file, contains the directions text. Saved in one place to help make uniform formating choices, etc.
#################

#' @name directionsModules
#' @export
RSECHelpText<-function(){ "This is RSEC... more to come"}


#' @rdname directionsModules
#' @export
clusterManyHelpText <- function() {
    tagList(
        h4("Directions:"),
        p("The user should first set the the core imputs. After this, the user can choose to navigate to other tabs to find different options to vary. Different options will appear depending on the core inputs you choose, so choose these first."),
        p("For all these inputs choosing multiple values means that clusterings with all these values will be tried in combination with all of the other values also already chosen (except some global, esoteric ones under 'Specialized options'). If you do not choose the option, the (single) default will be run. "),
        p("No clusterings will be calculated until you press 'Run This Code' to the right. Under the 'Run This Code' button , you can see how many clusterings will be run based on the options you have chosen so far. ")
    )
}

#' @rdname directionsModules
#' @export
combineManyHelpText <- function() {
    tagList(
        h3("Directions"),
        p("combineMany will combine the clusters found by clusterMany into a single clustering. This will be done by comparing how frequently the samples co-cluster, across the clusterings found in clusterMany.")
    )
}

#help text
#' @rdname directionsModules
#' @export
makeDendrogramHelpText <- function() {
     tagList(
        h3("Directions"),
        p("makeDendrogram will create a hiearchical clustering of the clusters found by combineMany, based on performing hiearchical clustering on the mediod of the cluster.")
    )
}

#helptext
#' @rdname directionsModules
#' @export
mergeClustersHelpText <- function() {
    tagList(
        h3("Directions"),
        p("mergeClusters will merge sister clusters on the dendrogram based on the percentage of differentially expressed genes found between the two clusters. It will continue up the tree, merging resulting groups, until reaching two clusterings that have more that the desired cutoff of DE genes.")
    )
}

#helptext
#' @rdname directionsModules
#' @export
plotClustersHelpText <- function() {
    tagList(
        h3("Directions"),
        helpText("plotClusters visualizes the cluster assignments of samples across several clusterings. The samples are ordered so as to align the clusterings from row to row.")
    )
}

#' @rdname InternalModules
#' @export
plotCoClusteringHelpText <- function() {
    tagList(
        h3("Directions"),
        helpText("plotCoClustering plots a heatmap of the percentage of times samples co-occur across different clusterings. These proportions are the values used to create unified clusters in the combineMany step. ")
    )
}

#help text
#' @rdname InternalModules
#' @export
plotDendrogramHelpText <- function() {
    tagList(
        h3("Directions"),
        helpText("plotDendrogram plots the hierarchical clustering of cluster mediods found by makeDendrogram.")
    )
}

#' @rdname InternalModules
#' @export
plotHeatmapHelpText <- function() {
    tagList(
        h3("Directions"),
        helpText("plotHeatmap plots a heatmap of the data (after appropriate transformation, if so indicated when uploading data), along with cluster assignments.")
    )
}