many more docs.

misc bugs

NAMESPACE

@@ -149,7 +149,6 @@ exportMethods(split)
 exportMethods(swapNameVariable)
 exportMethods(transformSignal)
 import(methods)
-import(pdist)
 import(shiny)
 importClassesFrom(S4Vectors,List)
 importClassesFrom(SummarizedExperiment,RangedSummarizedExperiment)

R/AllCommonParams.R

@@ -1,11 +1,19 @@
 doc_ct2 = function(){
-    "A ChIPtsne2 object"
+    "A ChIPtsne2 object."
 }
 
 doc_group_VAR = function(){
     "Attribute name to add to rowData for storing new row/region grouping assignment. Will be overwritten if it exists."
 }
 
 doc_return_group = function(){
- "Updated ChIPtsne2 object with group assignment added to rowData using specified group_VAR"
+ "Updated ChIPtsne2 object with group assignment added to rowData using specified group_VAR."
+}
+
+doc_extra_VARS = function(){
+    "Extra attributes from rowData or colData to carry through. These attributes will be available for facetting and similar ggplot2 operations."
+}
+
+doc_return_data = function(){
+    "If TRUE, no plot is returned but the final plotted data.frame is returned instead. Default is FALSE."
 }

R/class_ChIPtsne.R

@@ -41,9 +41,7 @@ ChIPtsne2 <- function(
 }
 
 #### Validity ####
-#' @importFrom S4Vectors setValidity2
-#' @importFrom BiocGenerics NCOL NROW
-S4Vectors::setValidity2("ChIPtsne2", function(object) {
+ct2_validity = function(object) {
     NR <- NROW(object)
     NC <- NCOL(object)
     msg <- NULL
@@ -70,7 +68,10 @@ S4Vectors::setValidity2("ChIPtsne2", function(object) {
     if (length(msg)) {
         msg
     } else TRUE
-})
+}
+#' @importFrom S4Vectors setValidity2
+#' @importFrom BiocGenerics NCOL NROW
+S4Vectors::setValidity2("ChIPtsne2", ct2_validity)
 
 #### Example data ####
 
@@ -206,19 +207,23 @@ addRegionAnnotation = function(ct2,
 
 #### replace rowRanges, names, dimnames ####
 
-setReplaceMethod("rowRanges", c("ChIPtsne2", "NULL"),
-                 function(x, ..., value){
-                     ChIPtsne2_no_rowRanges(
-                         assays = assays(x),
-                         rowData = rowData(x),
-                         colData = colData(x),
-                         rowToRowMat = x@rowToRowMat,
-                         colToRowMatCols = x@colToRowMatCols,
-                         name_VAR = x@name_VAR,
-                         position_VAR = x@position_VAR,
-                         value_VAR = x@value_VAR,
-                         region_VAR = x@region_VAR)
-                 }
-)
+ct2_replace_rowRanges = function(x, ..., value){
+    if(is.null(value)){
+        ChIPtsne2_no_rowRanges(
+            assays = assays(x),
+            rowData = rowData(x),
+            colData = colData(x),
+            rowToRowMat = x@rowToRowMat,
+            colToRowMatCols = x@colToRowMatCols,
+            name_VAR = x@name_VAR,
+            position_VAR = x@position_VAR,
+            value_VAR = x@value_VAR,
+            region_VAR = x@region_VAR)
+    }else{
+        stop("Manipulating rowRanges is not supported except for removal by NULL assignment.")
+    }
+}
+
+setReplaceMethod("rowRanges", c("ChIPtsne2", "NULL"), ct2_replace_rowRanges)
 
 

R/class_ChIPtsne_getset.R

@@ -68,16 +68,20 @@ setMethod("swapNameVariable", c("ChIPtsne2_no_rowRanges"), function(ct2, new_nam
     names(new_rn) = NULL
 
     rownames(r2rm) = new_rn
+    rowToRowMat(ct2) = r2rm
 
     old_assays = ct2@assays@data
     for(i in seq_along(old_assays)){
         rownames(old_assays[[i]]) = new_rn
     }
     ct2@assays = SummarizedExperiment::Assays(old_assays)
 
-    rowToRowMat(ct2) = r2rm
+
     if(is(ct2, "ChIPtsne2")){#unclear if equivalent operation of ChIPtsne2_no_rowRanges required
         names(ct2@rowRanges) = new_rn
+    }else{
+        rownames(ct2@elementMetadata) = new_rn
+        ct2@NAMES = new_rn
     }
     if(!is.null(new_name_VAR)){
         ct2@region_VAR = new_name_VAR

R/class_ChIPtsne_no_rowRanges.R

@@ -33,27 +33,29 @@ ChIPtsne2_no_rowRanges <- function(
 #' @export
 setGeneric("rowToRowMat", function(x, ...) standardGeneric("rowToRowMat"))
 
-#' @export
-setMethod("rowToRowMat", "ChIPtsne2_no_rowRanges", function(x, withDimnames=TRUE) {
+ct2_nrr_get_rowToRowMat = function(x, withDimnames=TRUE) {
     out <- x@rowToRowMat
     if (withDimnames)
         rownames(out) <- rownames(x)
     out
-})
+}
 
 #' @export
-setGeneric("colToRowMatCols", function(x, ...) standardGeneric("colToRowMatCols"))
+setMethod("rowToRowMat", "ChIPtsne2_no_rowRanges", ct2_nrr_get_rowToRowMat)
 
 #' @export
-setMethod("colToRowMatCols", "ChIPtsne2_no_rowRanges", function(x, withDimnames=TRUE) {
+setGeneric("colToRowMatCols", function(x, ...) standardGeneric("colToRowMatCols"))
+
+ct2_nrr_get_colToRowMatCols =  function(x, withDimnames=TRUE) {
     out <- x@colToRowMatCols
     out
-})
+}
+#' @export
+setMethod("colToRowMatCols", "ChIPtsne2_no_rowRanges", ct2_nrr_get_colToRowMatCols)
 
 #### Validity ####
-#' @importFrom S4Vectors setValidity2
-#' @importFrom BiocGenerics NCOL NROW
-S4Vectors::setValidity2("ChIPtsne2_no_rowRanges", function(object) {
+
+ct2_nrr_validity = function(object) {
     NR <- NROW(object)
     NC <- NCOL(object)
     msg <- NULL
@@ -73,20 +75,26 @@ S4Vectors::setValidity2("ChIPtsne2_no_rowRanges", function(object) {
     if (length(msg)) {
         msg
     } else TRUE
-})
+}
+
+#' @importFrom S4Vectors setValidity2
+#' @importFrom BiocGenerics NCOL NROW
+S4Vectors::setValidity2("ChIPtsne2_no_rowRanges", ct2_nrr_validity)
 
 #### Show ####
 
-#' @export
-#' @importMethodsFrom SummarizedExperiment show
-setMethod("show", "ChIPtsne2_no_rowRanges", function(object) {
+ct2_nrr_show = function(object) {
     callNextMethod()
     cat(
         "rowToRowMat has ", ncol(rowToRowMat(object)), " columns\n",
         "colToRowMatCols has ", length(colToRowMatCols(object)), " items\n",
         sep=""
     )
-})
+}
+
+#' @export
+#' @importMethodsFrom SummarizedExperiment show
+setMethod("show", "ChIPtsne2_no_rowRanges", ct2_nrr_show)
 
 #### Setter ####
 
@@ -95,29 +103,32 @@ setGeneric("rowToRowMat<-", function(x, ..., value)
     standardGeneric("rowToRowMat<-")
 )
 
-#' @export
-setReplaceMethod("rowToRowMat", "ChIPtsne2_no_rowRanges", function(x, value) {
+ct2_nrr_set_rowToRowMat = function(x, value) {
     x@rowToRowMat <- value
     validObject(x)
     x
-})
+}
+
+#' @export
+setReplaceMethod("rowToRowMat", "ChIPtsne2_no_rowRanges", ct2_nrr_set_rowToRowMat)
 
 #' @export
 setGeneric("colToRowMatCols<-", function(x, ..., value)
     standardGeneric("colToRowMatCols<-")
 )
 
-#' @export
-setReplaceMethod("colToRowMatCols", "ChIPtsne2_no_rowRanges", function(x, value) {
+ct2_nrr_set_colToRowMatCols = function(x, value) {
     x@colToRowMatCols <- value
     validObject(x)
     x
-})
+}
+
+#' @export
+setReplaceMethod("colToRowMatCols", "ChIPtsne2_no_rowRanges", ct2_nrr_set_colToRowMatCols)
 
 #### Subsetting by index ####
 
-#' @export
-setMethod("[", "ChIPtsne2_no_rowRanges", function(x, i, j, drop=TRUE) {
+ct2_nrr_index_accessor = function(x, i, j, drop=TRUE) {
     rrm <- rowToRowMat(x, withDimnames=FALSE)
     c2rrm = colToRowMatCols(x)
 
@@ -149,27 +160,13 @@ setMethod("[", "ChIPtsne2_no_rowRanges", function(x, i, j, drop=TRUE) {
                                 rowToRowMat = rrm,
                                 colToRowMatCols = c2rrm,
                                 check=FALSE)
-})
+}
+#' @export
+setMethod("[", "ChIPtsne2_no_rowRanges", ct2_nrr_index_accessor)
 
 #### split ####
 
-#' @param ChIPtsne2_no_rowRanges
-#'
-#' @export
-#' @examples
-#' split(ct2, "sample")
-#' split(ct2, colnames(ct2))
-#' split(ct2, "cell")
-#' split(ct2, "peak_MCF10CA1_CTCF")
-#' split(ct2, ct2$cell)
-#'
-#' sample_meta_data = getSampleMetaData(ct2)
-#' region_meta_data = getRegionMetaData(ct2)
-#'
-#' split(ct2, sample_meta_data$mark)
-#' split(ct2, region_meta_data$peak_MCF10A_CTCF)
-#'
-setMethod("split", "ChIPtsne2_no_rowRanges", function(x, f = NULL, drop=FALSE, ...){
+ct2_nrr_split = function(x, f = NULL, drop=FALSE, ...){
     mode = "by_column"
     sample_meta_data = getSampleMetaData(x)
     region_meta_data = getRegionMetaData(x)
@@ -202,7 +199,25 @@ setMethod("split", "ChIPtsne2_no_rowRanges", function(x, f = NULL, drop=FALSE, .
         x.split = lapply(f, function(split_val)x[split_val, ])
     }
     ChIPtsne2List(x.split)
-})
+}
+
+#' @param ChIPtsne2_no_rowRanges
+#'
+#' @export
+#' @examples
+#' split(ct2, "sample")
+#' split(ct2, colnames(ct2))
+#' split(ct2, "cell")
+#' split(ct2, "peak_MCF10CA1_CTCF")
+#' split(ct2, ct2$cell)
+#'
+#' sample_meta_data = getSampleMetaData(ct2)
+#' region_meta_data = getRegionMetaData(ct2)
+#'
+#' split(ct2, sample_meta_data$mark)
+#' split(ct2, region_meta_data$peak_MCF10A_CTCF)
+#'
+setMethod("split", "ChIPtsne2_no_rowRanges", ct2_nrr_split)
 
 .validate_names_match = function(args, dim_FUN, str){
     ref = args[[1]]
@@ -227,20 +242,7 @@ setMethod("split", "ChIPtsne2_no_rowRanges", function(x, f = NULL, drop=FALSE, .
 
 #### cbind ####
 
-#' @param ChIPtsne2_no_rowRanges
-#'
-#' @return
-#' @export
-#' @rdname cbind
-#'
-#' @examples
-#' ct2.left = exampleChIPtsne2()
-#' ct2.right = exampleChIPtsne2()
-#' colnames(ct2.right) = paste0("right_", colnames(ct2.right))
-#' ct2 = cbind(ct2.left, ct2.right)
-#' dim(ct2)
-#' colnames(ct2)
-setMethod("cbind", "ChIPtsne2_no_rowRanges", function(..., deparse.level=1) {
+ct2_nrr_cbind = function(..., deparse.level=1) {
     args <- list(...)
     .validate_names_unique(args, colnames, "Column")
     .validate_names_match(args, rownames, "Row")
@@ -273,24 +275,24 @@ setMethod("cbind", "ChIPtsne2_no_rowRanges", function(..., deparse.level=1) {
         rowToRowMat=all.rrm,
         colToRowMatCols=all.c2rrm,
         check=FALSE)
-})
-
+}
 
-#### rbind ####
 #' @param ChIPtsne2_no_rowRanges
 #'
-#' @return
+#' @return a ChIPtsne2 object of concatenated columns/samples of all items in input ChIPtsne2List
 #' @export
-#' @aliases rbind cbind
+#' @rdname cbind
 #'
 #' @examples
-#' ct2_a = exampleChIPtsne2()
-#' ct2_b = exampleChIPtsne2()
-#' # duplicated rownames are not allowed so we need to modify before rbind
-#' rownames(ct2_b) = paste0("b_", rownames(ct2_b))
-#' ct2_rbind = rbind(ct2_a, ct2_b)
-#' rownames(ct2_rbind)
-setMethod("rbind", "ChIPtsne2_no_rowRanges", function(..., deparse.level=1) {
+#' ct2.left = exampleChIPtsne2()
+#' ct2.right = exampleChIPtsne2()
+#' colnames(ct2.right) = paste0("right_", colnames(ct2.right))
+#' ct2 = cbind(ct2.left, ct2.right)
+#' dim(ct2)
+#' colnames(ct2)
+setMethod("cbind", "ChIPtsne2_no_rowRanges", ct2_nrr_cbind)
+
+ct2_nrr_rbind = function(..., deparse.level=1) {
     args <- list(...)
     .validate_names_unique(args, rownames, "Row")
     .validate_names_match(args, colnames, "Column")
@@ -318,12 +320,30 @@ setMethod("rbind", "ChIPtsne2_no_rowRanges", function(..., deparse.level=1) {
         out,
         rowToRowMat=all.rrm,
         check=FALSE)
-})
-
-setReplaceMethod("dimnames", c("ChIPtsne2_no_rowRanges", "list"),
-                 function(x, value)
-                 {
-                     x = .update_ct2_rownames(x, new_names = value[[1]])
-                     x = .update_ct2_colnames(x, new_names = value[[2]])
-                     x
-                 })
+}
+
+
+#### rbind ####
+#' @param ChIPtsne2_no_rowRanges
+#'
+#' @return a ChIPtsne2 object of concatenated rows/regions of all items in input ChIPtsne2List
+#' @export
+#' @aliases rbind cbind
+#'
+#' @examples
+#' ct2_a = exampleChIPtsne2()
+#' ct2_b = exampleChIPtsne2()
+#' # duplicated rownames are not allowed so we need to modify before rbind
+#' rownames(ct2_b) = paste0("b_", rownames(ct2_b))
+#' ct2_rbind = rbind(ct2_a, ct2_b)
+#' rownames(ct2_rbind)
+setMethod("rbind", "ChIPtsne2_no_rowRanges", ct2_nrr_rbind)
+
+ct2_nrr_set_dimnames =  function(x, value){
+    x = .update_ct2_rownames(x, new_names = value[[1]])
+    x = .update_ct2_colnames(x, new_names = value[[2]])
+    x
+}
+
+setReplaceMethod("dimnames", c("ChIPtsne2_no_rowRanges", "list"), ct2_nrr_set_dimnames)
+