rowLinks {TreeSummarizedExperiment} | R Documentation |
All accessor functions that work on
SingleCellExperiment
should work on TreeSummarizedExperiment. Additionally, new accessors
rowLinks
colLinks
, rowTree
and colTree
accessor
function are available for TreeSummarizedExperiment.
rowLinks(x) ## S4 method for signature 'TreeSummarizedExperiment' rowLinks(x) colLinks(x) ## S4 method for signature 'TreeSummarizedExperiment' colLinks(x) rowTree(x, whichTree = 1, value) ## S4 method for signature 'TreeSummarizedExperiment' rowTree(x, whichTree = 1, value) rowTree(x, whichTree = 1) <- value ## S4 replacement method for signature 'TreeSummarizedExperiment' rowTree(x, whichTree = 1) <- value colTree(x, whichTree = 1) ## S4 method for signature 'TreeSummarizedExperiment' colTree(x, whichTree = 1) colTree(x, whichTree = 1) <- value ## S4 replacement method for signature 'TreeSummarizedExperiment' colTree(x, whichTree = 1) <- value rowTreeNames(x, value) ## S4 method for signature 'TreeSummarizedExperiment' rowTreeNames(x, value) rowTreeNames(x) <- value ## S4 replacement method for signature 'TreeSummarizedExperiment' rowTreeNames(x) <- value colTreeNames(x, value) ## S4 method for signature 'TreeSummarizedExperiment' colTreeNames(x, value) colTreeNames(x) <- value ## S4 replacement method for signature 'TreeSummarizedExperiment' colTreeNames(x) <- value referenceSeq(x) ## S4 method for signature 'TreeSummarizedExperiment' referenceSeq(x) referenceSeq(x) <- value ## S4 replacement method for signature 'TreeSummarizedExperiment' referenceSeq(x) <- value ## S4 method for signature 'TreeSummarizedExperiment,ANY,ANY,ANY' x[i, j, ..., drop = TRUE] ## S4 replacement method for signature ## 'TreeSummarizedExperiment,ANY,ANY,TreeSummarizedExperiment' x[i, j, ...] <- value ## S4 replacement method for signature 'TreeSummarizedExperiment' rownames(x) <- value ## S4 replacement method for signature 'TreeSummarizedExperiment' colnames(x) <- value subsetByLeaf( x, rowLeaf, colLeaf, whichRowTree, whichColTree, updateTree = TRUE ) ## S4 method for signature 'TreeSummarizedExperiment' subsetByLeaf( x, rowLeaf, colLeaf, whichRowTree, whichColTree, updateTree = TRUE ) subsetByNode(x, rowNode, colNode, whichRowTree, whichColTree) ## S4 method for signature 'TreeSummarizedExperiment' subsetByNode(x, rowNode, colNode, whichRowTree, whichColTree)
x |
A TreeSummarizedExperiment object |
whichTree |
A numeric indicator or name character to specify which tree
in the |
value |
|
i, j |
The row, column index to subset |
... |
The argument from the subset function |
drop |
A logical value, TRUE or FALSE. The argument from the subset
function |
rowLeaf |
A vector of leaves that are used to subset rows. One could use the leaf number, or the leaf label to specify nodes, but not a mixture of them. |
colLeaf |
A vector of leaves that are used to subset columns. One could use the leaf number, or the leaf label to specify nodes, but not a mixture of them. |
whichRowTree |
A numeric indicator or name character to specify which tree
in the |
whichColTree |
A numeric indicator or name character to specify which tree
in the |
updateTree |
TRUE or FALSE. Default is TRUE, which updates tree structures after subsetting. |
rowNode |
A vector of nodes that are used to subset rows. One could use the node number, the node label or the node alias to specify nodes, but not a mixture of them. |
colNode |
A vector of nodes that are used to subset columns. One could use the node number, the node label or the node alias to specify nodes, but not a mixture of them. |
Elements from TreeSummarizedExperiment
.
Ruizhu HUANG
TreeSummarizedExperiment
SingleCellExperiment
# the assay table set.seed(1) y <- matrix(rnbinom(300,size=1,mu=10),nrow=10) colnames(y) <- paste(rep(LETTERS[1:3], each = 10), rep(1:10,3), sep = "_") rownames(y) <- tinyTree$tip.label # the row data rowInf <- DataFrame(var1 = sample(letters[1:3], 10, replace = TRUE), var2 = sample(c(TRUE, FALSE), 10, replace = TRUE)) # the column data colInf <- DataFrame(gg = factor(sample(1:3, 30, replace = TRUE)), group = rep(LETTERS[1:3], each = 10)) # the tree structure on the rows of assay tables data("tinyTree") # the tree structure on the columns of assay tables sampTree <- ape::rtree(30) sampTree$tip.label <- colnames(y) # create the TreeSummarizedExperiment object toy_tse <- TreeSummarizedExperiment(assays = list(y), rowData = rowInf, colData = colInf, rowTree = tinyTree, colTree = sampTree) ## extract the rowData (rowD <- rowData(x = toy_tse)) ## extract the colData (colD <- colData(x = toy_tse)) ## extract the linkData # on rows (rowL <- rowLinks(x = toy_tse)) # on columns (colL <- colLinks(x = toy_tse)) ## extract the treeData # on rows (rowT <- rowTree(x = toy_tse)) # on columns (colT <- colTree(x = toy_tse)) # the referenceSeq data refSeq <- DNAStringSetList(one = DNAStringSet(rep("A",nrow(toy_tse))), two = DNAStringSet(rep("B",nrow(toy_tse)))) referenceSeq(toy_tse) <- refSeq toy_tse # subset treeSE by leaves library(ape) set.seed(1) z <- makeTSE(nrow = 5, ncol = 4, include.rowTree = TRUE, include.colTree = FALSE) y <- makeTSE(nrow = 4, ncol = 4, include.rowTree = TRUE, include.colTree = FALSE) tr <- ape::rtree(4) zy <- rbind(z, y) x <- changeTree(x = zy, rowTree = tr, whichRowTree = 2, rowNodeLab = tr$tip.label) rowLinks(zy) rowLinks(x) ## 1) rowLeaf exist only in one of trees rf <- c("t1", "t3") sx <- subsetByLeaf(x = x, rowLeaf = rf) rowLinks(sx) sx <- subsetByLeaf(x = x, rowLeaf = rf, updateTree = FALSE) rowLinks(sx) ## 2) rowLeaf exist in all trees rf <- 1:3 sxx <- subsetByLeaf(x = x, rowLeaf = rf) rowLinks(sxx) ## 3) rowLeaf exist in all trees, but subset and update only the specified trees rf <- c(3:4) sxx <- subsetByLeaf(x = x, rowLeaf = rf, whichRowTree = "phylo") rowLinks(sxx)