@@ -9,6 +9,7 @@ Description: celda leverages Bayesian hierarchical modeling to cluster genes,

 Depends:

     R (>= 3.2.2)

 Imports:

+    plyr,

     dplyr,

     foreach,

     gtools,

@@ -46,6 +46,7 @@ export(getK)

 export(getL)

 export(getModel)

 export(normalizeCounts)

+export(recode_cluster_labels)

 export(render_celda_heatmap)

 export(render_interactive_kl_plot)

 export(render_iteration_likelihood_plot)

@@ -100,6 +100,36 @@ reorder.labels.by.size.then.counts = function(counts, z, y, K, L) {

 }  

+#' Re-code cluster label by provided mapping scheme

+#' 

+#' This function will re-code cluster labels based off of a mapping provided by the user,

+#' for all fields on a celda object involving cluster labels.

+#' e.g. if Z values range from 1-4 and the user would like all 3's switched to 1's and

+#' vice versa, this function can be useful. NOTE: it is recommended that this function's results

+#' aren't used to overwrite the original celda model object provided, in the event of a mis-mapping.

+#' 

+#' @param celda.mod An object of class celda_C, celda_G, or celda_CG

+#' @param from A numeric vector of the "keys", corresponding to the "values" in the to parameter

+#' @param to A numeric vector of the "values"; what each corresponding number in "from" should be mapped to

+#' @export

+recode_cluster_labels = function(celda.mod, from, to) {

+  # Make sure that every value gets a replacement

+  if (length(setdiff(from, to)) != 0) {

+    stop("All values in 'from' must have a mapping in 'to'")

+  }

+  

+  if (class(celda.mod) %in% c("celda_C", "celda_CG")) {

+    celda.mod$z = plyr::mapvalues(celda.mod$z, from, to)

+    celda.mod$z.probability = celda.mod$z.probability[, to]

+  }

+  if (class(celda.mod) %in% c("celda_G", "celda_CG")) {

+    celda.mod$y = plyr::mapvalues(celda.mod$y, from, to)

+    celda.mod$y.probability = celda.mod$y.probability[, to]

+  }

+  return(celda.mod)

+}

+

+

 #' Check whether a count matrix was the one used in a given celda run

 #' 

 #' Compare the MD5 checksum of a provided count.matrix to the count matrix

new file mode 100755

@@ -0,0 +1,22 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/celda_functions.R

+\name{recode_cluster_labels}

+\alias{recode_cluster_labels}

+\title{Re-code cluster label by provided mapping scheme}

+\usage{

+recode_cluster_labels(celda.mod, from, to)

+}

+\arguments{

+\item{celda.mod}{An object of class celda_C, celda_G, or celda_CG}

+

+\item{from}{A numeric vector of the "keys", corresponding to the "values" in the to parameter}

+

+\item{to}{A numeric vector of the "values"; what each corresponding number in "from" should be mapped to}

+}

+\description{

+This function will re-code cluster labels based off of a mapping provided by the user,

+for all fields on a celda object involving cluster labels.

+e.g. if Z values range from 1-4 and the user would like all 3's switched to 1's and

+vice versa, this function can be useful. NOTE: it is recommended that this function's results

+aren't used to overwrite the original celda model object provided, in the event of a mis-mapping.

+}