... | ... |
@@ -1,6 +1,6 @@ |
1 | 1 |
Package: celda |
2 | 2 |
Title: CEllular Latent Dirichlet Allocation |
3 |
-Version: 1.5.10 |
|
3 |
+Version: 1.5.11 |
|
4 | 4 |
Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu", |
5 | 5 |
role = c("aut", "cre")), |
6 | 6 |
person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")), |
... | ... |
@@ -8,10 +8,10 @@ |
8 | 8 |
#' \item A \linkS4class{SingleCellExperiment} object returned by |
9 | 9 |
#' \link{celda_C}, or \link{celda_CG}, with the matrix |
10 | 10 |
#' located in the \code{useAssay} assay slot. The |
11 |
-#' a \link[SingleCellExperiment]{altExp} slot with name \code{altExpName} will |
|
11 |
+#' a \link{altExp} slot with name \code{altExpName} will |
|
12 | 12 |
#' be used. Rows represent features and columns represent cells. |
13 | 13 |
#' \item Celda model object.} |
14 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
14 |
+#' @param altExpName The name for the \link{altExp} slot |
|
15 | 15 |
#' to use. Default "featureSubset". |
16 | 16 |
#' @param value Character vector of cell cluster labels for replacements. Works |
17 | 17 |
#' only if \code{x} is a \linkS4class{SingleCellExperiment} object. |
... | ... |
@@ -85,7 +85,7 @@ setReplaceMethod("celdaClusters", signature(x = "SingleCellExperiment"), |
85 | 85 |
#' \link{celda_G}, or \link{celda_CG}, with the matrix |
86 | 86 |
#' located in the \code{useAssay} assay slot. |
87 | 87 |
#' Rows represent features and columns represent cells. |
88 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
88 |
+#' @param altExpName The name for the \link{altExp} slot |
|
89 | 89 |
#' to use. Default "featureSubset". |
90 | 90 |
#' @param value Character vector of feature module labels for replacements. |
91 | 91 |
#' Works only if \code{x} is a \linkS4class{SingleCellExperiment} object. |
... | ... |
@@ -141,7 +141,7 @@ setReplaceMethod("celdaModules", signature(sce = "SingleCellExperiment"), |
141 | 141 |
#' located in the \code{useAssay} assay slot. |
142 | 142 |
#' Rows represent features and columns represent cells. |
143 | 143 |
#' \item A celda model object.} |
144 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
144 |
+#' @param altExpName The name for the \link{altExp} slot |
|
145 | 145 |
#' to use. Default "featureSubset". |
146 | 146 |
#' @param value Character vector of sample labels for replacements. Works |
147 | 147 |
#' only is \code{x} is a \linkS4class{SingleCellExperiment} object. |
... | ... |
@@ -263,7 +263,7 @@ setMethod("matrixNames", |
263 | 263 |
#' priors from the celdaList object when it was created. |
264 | 264 |
#' @param x An object of class \linkS4class{SingleCellExperiment} or class |
265 | 265 |
#' \code{celdaList}. |
266 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
266 |
+#' @param altExpName The name for the \link{altExp} slot |
|
267 | 267 |
#' to use. Default "featureSubset". |
268 | 268 |
#' @param ... Ignored. Placeholder to prevent check warning. |
269 | 269 |
#' @return Data Frame. Contains details on the various K/L parameters, chain |
... | ... |
@@ -310,7 +310,7 @@ setMethod("runParams", |
310 | 310 |
#' \link{celdaGridSearch} run. |
311 | 311 |
#' @param x An object of class \linkS4class{SingleCellExperiment} or |
312 | 312 |
#' \code{celdaList}. |
313 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
313 |
+#' @param altExpName The name for the \link{altExp} slot |
|
314 | 314 |
#' to use. Default "featureSubset". |
315 | 315 |
#' @param ... Ignored. Placeholder to prevent check warning. |
316 | 316 |
#' @return List. Contains one celdaModel object for each of the parameters |
... | ... |
@@ -357,7 +357,7 @@ setMethod("resList", |
357 | 357 |
#' \link{celda_C}, \link{celda_G} or \link{celda_CG}. |
358 | 358 |
#' @param sce A \link[SingleCellExperiment]{SingleCellExperiment} object |
359 | 359 |
#' returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}. |
360 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
360 |
+#' @param altExpName The name for the \link{altExp} slot |
|
361 | 361 |
#' to use. Default "featureSubset". |
362 | 362 |
#' @param ... Ignored. Placeholder to prevent check warning. |
363 | 363 |
#' @return Character. The celda model. Can be one of "celda_C", "celda_G", or |
... | ... |
@@ -12,8 +12,8 @@ |
12 | 12 |
#' with the matrix located in the assay slot under \code{useAssay}. |
13 | 13 |
#' Rows represent features and columns represent cells. |
14 | 14 |
#' @param useAssay A string specifying the name of the |
15 |
-#' \link[SummarizedExperiment]{assay} slot to use. Default "counts". |
|
16 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
15 |
+#' \link{assay} slot to use. Default "counts". |
|
16 |
+#' @param altExpName The name for the \link{altExp} slot |
|
17 | 17 |
#' to use. Default "featureSubset". |
18 | 18 |
#' @param model Celda model. Options available in \link{availableModels}. |
19 | 19 |
#' @param paramsTest List. A list denoting the combinations of parameters to |
... | ... |
@@ -45,7 +45,7 @@ |
45 | 45 |
#' and main process. Default "Celda". |
46 | 46 |
#' @return A \linkS4class{SingleCellExperiment} object. Function |
47 | 47 |
#' parameter settings and celda model results are stored in the |
48 |
-#' \link[S4Vectors]{metadata} \code{"celda_grid_search"} slot. |
|
48 |
+#' \link{metadata} \code{"celda_grid_search"} slot. |
|
49 | 49 |
#' @param ... Ignored. Placeholder to prevent check warning. |
50 | 50 |
#' @seealso \link{celda_G} for feature clustering, \link{celda_C} for |
51 | 51 |
#' clustering of cells, and \link{celda_CG} for simultaneous clustering of |
... | ... |
@@ -440,7 +440,7 @@ setMethod("celdaGridSearch", |
440 | 440 |
#' \item celdaList object.} |
441 | 441 |
#' @param params List. List of parameters used to subset the matching celda |
442 | 442 |
#' models in list \code{"celda_grid_search"} in \code{metadata(x)}. |
443 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
443 |
+#' @param altExpName The name for the \link{altExp} slot |
|
444 | 444 |
#' to use. Default "featureSubset". |
445 | 445 |
#' @param ... Ignored. Placeholder to prevent check warning. |
446 | 446 |
#' @return One of |
... | ... |
@@ -451,10 +451,10 @@ setMethod("celdaGridSearch", |
451 | 451 |
#' \code{"celda_grid_search"} slot in \code{metadata(x)} matches |
452 | 452 |
#' the given criteria, a new \linkS4class{SingleCellExperiment} object |
453 | 453 |
#' with the matching model stored in the |
454 |
-#' \link[S4Vectors]{metadata} |
|
454 |
+#' \link{metadata} |
|
455 | 455 |
#' \code{"celda_parameters"} slot will be returned. Otherwise, a new |
456 | 456 |
#' \linkS4class{SingleCellExperiment} object with the subset models stored |
457 |
-#' in the \link[S4Vectors]{metadata} |
|
457 |
+#' in the \link{metadata} |
|
458 | 458 |
#' \code{"celda_grid_search"} slot will be returned. |
459 | 459 |
#' \item A new \code{celdaList} object containing all models matching the |
460 | 460 |
#' provided criteria in \code{params}. If only one item in the |
... | ... |
@@ -581,7 +581,7 @@ setMethod("subsetCeldaList", |
581 | 581 |
#' best model as a |
582 | 582 |
#' \code{celdaList} object or not. If \code{FALSE}, return the best model as a |
583 | 583 |
#' corresponding celda model object. |
584 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
584 |
+#' @param altExpName The name for the \link{altExp} slot |
|
585 | 585 |
#' to use. Default "featureSubset". |
586 | 586 |
#' @param ... Ignored. Placeholder to prevent check warning. |
587 | 587 |
#' @return One of |
... | ... |
@@ -591,10 +591,10 @@ setMethod("subsetCeldaList", |
591 | 591 |
#' \code{metadata(x)}. If there is only one set of parameters, |
592 | 592 |
#' a new \linkS4class{SingleCellExperiment} object |
593 | 593 |
#' with the matching model stored in the |
594 |
-#' \link[S4Vectors]{metadata} |
|
594 |
+#' \link{metadata} |
|
595 | 595 |
#' \code{"celda_parameters"} slot will be returned. Otherwise, a new |
596 | 596 |
#' \linkS4class{SingleCellExperiment} object with the subset models stored |
597 |
-#' in the \link[S4Vectors]{metadata} |
|
597 |
+#' in the \link{metadata} |
|
598 | 598 |
#' \code{"celda_grid_search"} slot will be returned. |
599 | 599 |
#' \item A new \code{celdaList} object containing one model with the best |
600 | 600 |
#' log-likelihood for each set of parameters. If only one set of parameters |
... | ... |
@@ -4,9 +4,9 @@ |
4 | 4 |
#' populations and samples). |
5 | 5 |
#' @param sce A \link[SingleCellExperiment]{SingleCellExperiment} object |
6 | 6 |
#' returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}. |
7 |
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} |
|
7 |
+#' @param useAssay A string specifying which \link{assay} |
|
8 | 8 |
#' slot to use. Default "counts". |
9 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
9 |
+#' @param altExpName The name for the \link{altExp} slot |
|
10 | 10 |
#' to use. Default "featureSubset". |
11 | 11 |
#' @param level Character. One of "cellPopulation" or "Sample". |
12 | 12 |
#' "cellPopulation" will display the absolute probabilities and relative |
... | ... |
@@ -8,9 +8,9 @@ |
8 | 8 |
#' transformed before applying UMAP. |
9 | 9 |
#' @param sce A \link[SingleCellExperiment]{SingleCellExperiment} object |
10 | 10 |
#' returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}. |
11 |
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} |
|
11 |
+#' @param useAssay A string specifying which \link{assay} |
|
12 | 12 |
#' slot to use. Default "counts". |
13 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
13 |
+#' @param altExpName The name for the \link{altExp} slot |
|
14 | 14 |
#' to use. Default "featureSubset". |
15 | 15 |
#' @param maxCells Integer. Maximum number of cells to plot. Cells will be |
16 | 16 |
#' randomly subsampled if \code{ncol(sce) > maxCells}. Larger numbers of cells |
... | ... |
@@ -62,7 +62,7 @@ |
62 | 62 |
#' @param ... Additional parameters to pass to \link[uwot]{umap}. |
63 | 63 |
#' @return \code{sce} with UMAP coordinates |
64 | 64 |
#' (columns "celda_UMAP1" & "celda_UMAP2") added to |
65 |
-#' \code{\link[SingleCellExperiment]{reducedDim}(sce, "celda_UMAP")}. |
|
65 |
+#' \code{\link{reducedDim}(sce, "celda_UMAP")}. |
|
66 | 66 |
#' @export |
67 | 67 |
setGeneric("celdaUmap", |
68 | 68 |
function(sce, ...) { |
... | ... |
@@ -1,10 +1,10 @@ |
1 | 1 |
#' @title Cell clustering with Celda |
2 | 2 |
#' @description Clusters the columns of a count matrix containing single-cell |
3 | 3 |
#' data into K subpopulations. The |
4 |
-#' \code{useAssay} \link[SummarizedExperiment]{assay} slot in |
|
5 |
-#' \code{altExpName} \link[SingleCellExperiment]{altExp} slot will be used if |
|
4 |
+#' \code{useAssay} \link{assay} slot in |
|
5 |
+#' \code{altExpName} \link{altExp} slot will be used if |
|
6 | 6 |
#' it exists. Otherwise, the \code{useAssay} |
7 |
-#' \link[SummarizedExperiment]{assay} slot in \code{x} will be used if |
|
7 |
+#' \link{assay} slot in \code{x} will be used if |
|
8 | 8 |
#' \code{x} is a \linkS4class{SingleCellExperiment} object. |
9 | 9 |
#' @param x A numeric \link{matrix} of counts or a |
10 | 10 |
#' \linkS4class{SingleCellExperiment} |
... | ... |
@@ -12,8 +12,8 @@ |
12 | 12 |
#' \code{altExp(x, altExpName)}. |
13 | 13 |
#' Rows represent features and columns represent cells. |
14 | 14 |
#' @param useAssay A string specifying the name of the |
15 |
-#' \link[SummarizedExperiment]{assay} slot to use. Default "counts". |
|
16 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
15 |
+#' \link{assay} slot to use. Default "counts". |
|
16 |
+#' @param altExpName The name for the \link{altExp} slot |
|
17 | 17 |
#' to use. Default "featureSubset". |
18 | 18 |
#' @param sampleLabel Vector or factor. Denotes the sample label for each cell |
19 | 19 |
#' (column) in the count matrix. |
... | ... |
@@ -59,10 +59,10 @@ |
59 | 59 |
#' @param verbose Logical. Whether to print log messages. Default TRUE. |
60 | 60 |
#' @param ... Ignored. Placeholder to prevent check warning. |
61 | 61 |
#' @return A \link[SingleCellExperiment]{SingleCellExperiment} object. Function |
62 |
-#' parameter settings are stored in the \link[S4Vectors]{metadata} |
|
62 |
+#' parameter settings are stored in the \link{metadata} |
|
63 | 63 |
#' \code{"celda_parameters"} slot. |
64 | 64 |
#' Columns \code{celda_sample_label} and \code{celda_cell_cluster} in |
65 |
-#' \link[SummarizedExperiment]{colData} contain sample labels and celda cell |
|
65 |
+#' \link{colData} contain sample labels and celda cell |
|
66 | 66 |
#' population clusters. |
67 | 67 |
#' @seealso \link{celda_G} for feature clustering and \link{celda_CG} for |
68 | 68 |
#' simultaneous clustering of features and cells. \link{celdaGridSearch} can |
... | ... |
@@ -1,19 +1,19 @@ |
1 | 1 |
#' @title Cell and feature clustering with Celda |
2 | 2 |
#' @description Clusters the rows and columns of a count matrix containing |
3 | 3 |
#' single-cell data into L modules and K subpopulations, respectively. The |
4 |
-#' \code{useAssay} \link[SummarizedExperiment]{assay} slot in |
|
5 |
-#' \code{altExpName} \link[SingleCellExperiment]{altExp} slot will be used if |
|
4 |
+#' \code{useAssay} \link{assay} slot in |
|
5 |
+#' \code{altExpName} \link{altExp} slot will be used if |
|
6 | 6 |
#' it exists. Otherwise, the \code{useAssay} |
7 |
-#' \link[SummarizedExperiment]{assay} slot in \code{x} will be used if |
|
7 |
+#' \link{assay} slot in \code{x} will be used if |
|
8 | 8 |
#' \code{x} is a \linkS4class{SingleCellExperiment} object. |
9 | 9 |
#' @param x A numeric \link{matrix} of counts or a |
10 | 10 |
#' \linkS4class{SingleCellExperiment} |
11 |
-#' with the matrix located in the \link[SummarizedExperiment]{assay} |
|
11 |
+#' with the matrix located in the \link{assay} |
|
12 | 12 |
#' slot under \code{useAssay} in \code{altExp(x, altExpName)}. |
13 | 13 |
#' Rows represent features and columns represent cells. |
14 | 14 |
#' @param useAssay A string specifying the name of the |
15 |
-#' \link[SummarizedExperiment]{assay} slot to use. Default "counts". |
|
16 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
15 |
+#' \link{assay} slot to use. Default "counts". |
|
16 |
+#' @param altExpName The name for the \link{altExp} slot |
|
17 | 17 |
#' to use. Default "featureSubset". |
18 | 18 |
#' @param sampleLabel Vector or factor. Denotes the sample label for each cell |
19 | 19 |
#' (column) in the count matrix. |
... | ... |
@@ -35,11 +35,12 @@ |
35 | 35 |
#' likelihood to stop inference. Default 10. |
36 | 36 |
#' @param maxIter Integer. Maximum number of iterations of Gibbs sampling to |
37 | 37 |
#' perform. Default 200. |
38 |
-#' @param splitOnIter Integer. On every `splitOnIter` iteration, a heuristic |
|
38 |
+#' @param splitOnIter Integer. On every \code{splitOnIter} iteration, |
|
39 |
+#' a heuristic |
|
39 | 40 |
#' will be applied to determine if a cell population or feature module should |
40 | 41 |
#' be reassigned and another cell population or feature module should be split |
41 | 42 |
#' into two clusters. To disable splitting, set to -1. Default 10. |
42 |
-#' @param splitOnLast Integer. After `stopIter` iterations have been |
|
43 |
+#' @param splitOnLast Integer. After \code{stopIter} iterations have been |
|
43 | 44 |
#' performed without improvement, a heuristic will be applied to determine if |
44 | 45 |
#' a cell population or feature module should be reassigned and another cell |
45 | 46 |
#' population or feature module should be split into two clusters. If a split |
... | ... |
@@ -52,32 +53,32 @@ |
52 | 53 |
#' With 'random', cells are randomly assigned to a populations. With 'split', |
53 | 54 |
#' cells will be split into sqrt(K) populations and then each popluation will |
54 | 55 |
#' be subsequently split into another sqrt(K) populations. With 'predefined', |
55 |
-#' values in `zInit` will be used to initialize `z`. Default 'split'. |
|
56 |
+#' values in \code{zInit} will be used to initialize \code{z}. Default 'split'. |
|
56 | 57 |
#' @param yInitialize Chararacter. One of 'random', 'split', or 'predefined'. |
57 | 58 |
#' With 'random', features are randomly assigned to a modules. With 'split', |
58 | 59 |
#' features will be split into sqrt(L) modules and then each module will be |
59 | 60 |
#' subsequently split into another sqrt(L) modules. With 'predefined', values |
60 |
-#' in `yInit` will be used to initialize `y`. Default 'split'. |
|
61 |
+#' in \code{yInit} will be used to initialize \code{y}. Default 'split'. |
|
61 | 62 |
#' @param zInit Integer vector. Sets initial starting values of z. If NULL, |
62 | 63 |
#' starting values for each cell will be randomly sampled from 1:K. 'zInit' |
63 |
-#' can only be used when `initialize' = 'random'`. Default NULL. |
|
64 |
+#' can only be used when \code{initialize = "random"}. Default NULL. |
|
64 | 65 |
#' @param yInit Integer vector. Sets initial starting values of y. If NULL, |
65 | 66 |
#' starting values for each feature will be randomly sampled from 1:L. |
66 |
-#' 'yInit' can only be used when `initialize = 'random'`. Default NULL. |
|
67 |
-#' @param countChecksum Character. An MD5 checksum for the `counts` matrix. |
|
67 |
+#' 'yInit' can only be used when \code{initialize = "random"}. Default NULL. |
|
68 |
+#' @param countChecksum Character. An MD5 checksum for the counts matrix. |
|
68 | 69 |
#' Default NULL. |
69 | 70 |
#' @param logfile Character. Messages will be redirected to a file named |
70 | 71 |
#' `logfile`. If NULL, messages will be printed to stdout. Default NULL. |
71 | 72 |
#' @param verbose Logical. Whether to print log messages. Default TRUE. |
72 | 73 |
#' @param ... Ignored. Placeholder to prevent check warning. |
73 | 74 |
#' @return A \linkS4class{SingleCellExperiment} object. Function |
74 |
-#' parameter settings are stored in \link[S4Vectors]{metadata} |
|
75 |
-#' \code{"celda_parameters"} in \link[SingleCellExperiment]{altExp} slot. |
|
76 |
-#' In \link[SingleCellExperiment]{altExp} slot, |
|
75 |
+#' parameter settings are stored in \link{metadata} |
|
76 |
+#' \code{"celda_parameters"} in \link{altExp} slot. |
|
77 |
+#' In \link{altExp} slot, |
|
77 | 78 |
#' columns \code{celda_sample_label} and \code{celda_cell_cluster} in |
78 |
-#' \link[SummarizedExperiment]{colData} contain sample labels and celda cell |
|
79 |
+#' \link{colData} contain sample labels and celda cell |
|
79 | 80 |
#' population clusters. Column \code{celda_feature_module} in |
80 |
-#' \link[SummarizedExperiment]{rowData} contains feature modules. |
|
81 |
+#' \link{rowData} contains feature modules. |
|
81 | 82 |
#' @seealso \link{celda_G} for feature clustering and \link{celda_C} for |
82 | 83 |
#' clustering cells. \link{celdaGridSearch} can be used to run multiple |
83 | 84 |
#' values of K/L and multiple chains in parallel. |
... | ... |
@@ -1,18 +1,18 @@ |
1 | 1 |
#' @title Feature clustering with Celda |
2 | 2 |
#' @description Clusters the rows of a count matrix containing single-cell data |
3 | 3 |
#' into L modules. The |
4 |
-#' \code{useAssay} \link[SummarizedExperiment]{assay} slot in |
|
5 |
-#' \code{altExpName} \link[SingleCellExperiment]{altExp} slot will be used if |
|
4 |
+#' \code{useAssay} \link{assay} slot in |
|
5 |
+#' \code{altExpName} \link{altExp} slot will be used if |
|
6 | 6 |
#' it exists. Otherwise, the \code{useAssay} |
7 |
-#' \link[SummarizedExperiment]{assay} slot in \code{x} will be used if |
|
7 |
+#' \link{assay} slot in \code{x} will be used if |
|
8 | 8 |
#' \code{x} is a \linkS4class{SingleCellExperiment} object. |
9 | 9 |
#' @param x A numeric \link{matrix} of counts or a |
10 | 10 |
#' \linkS4class{SingleCellExperiment} |
11 | 11 |
#' with the matrix located in the assay slot under \code{useAssay}. |
12 | 12 |
#' Rows represent features and columns represent cells. |
13 | 13 |
#' @param useAssay A string specifying the name of the |
14 |
-#' \link[SummarizedExperiment]{assay} slot to use. Default "counts". |
|
15 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
14 |
+#' \link{assay} slot to use. Default "counts". |
|
15 |
+#' @param altExpName The name for the \link{altExp} slot |
|
16 | 16 |
#' to use. Default "featureSubset". |
17 | 17 |
#' @param L Integer. Number of feature modules. |
18 | 18 |
#' @param beta Numeric. Concentration parameter for Phi. Adds a pseudocount to |
... | ... |
@@ -53,9 +53,9 @@ |
53 | 53 |
#' @param verbose Logical. Whether to print log messages. Default TRUE. |
54 | 54 |
#' @param ... Ignored. Placeholder to prevent check warning. |
55 | 55 |
#' @return A \linkS4class{SingleCellExperiment} object. Function |
56 |
-#' parameter settings are stored in the \link[S4Vectors]{metadata} |
|
56 |
+#' parameter settings are stored in the \link{metadata} |
|
57 | 57 |
#' \code{"celda_parameters"} slot. Column \code{celda_feature_module} in |
58 |
-#' \link[SummarizedExperiment]{rowData} contains feature modules. |
|
58 |
+#' \link{rowData} contains feature modules. |
|
59 | 59 |
#' @seealso \link{celda_C} for cell clustering and \link{celda_CG} for |
60 | 60 |
#' simultaneous clustering of features and cells. \link{celdaGridSearch} can |
61 | 61 |
#' be used to run multiple values of L and multiple chains in parallel. |
... | ... |
@@ -137,7 +137,7 @@ normalizeCounts <- function(counts, |
137 | 137 |
#' @param sce \linkS4class{SingleCellExperiment} object returned from |
138 | 138 |
#' \link{celda_C} or \link{celda_CG}. Must contain column |
139 | 139 |
#' \code{celda_cell_cluster} in |
140 |
-#' \code{\link[SummarizedExperiment]{colData}(altExp(sce, altExpName))}. |
|
140 |
+#' \code{\link{colData}(altExp(sce, altExpName))}. |
|
141 | 141 |
#' @param from Numeric vector. Unique values in the range of |
142 | 142 |
#' \code{seq(celdaClusters(sce, altExpName = altExpName))} that correspond to |
143 | 143 |
#' the original cluster |
... | ... |
@@ -145,7 +145,7 @@ normalizeCounts <- function(counts, |
145 | 145 |
#' @param to Numeric vector. Unique values in the range of |
146 | 146 |
#' \code{seq(celdaClusters(sce, altExpName = altExpName))} that correspond to |
147 | 147 |
#' the new cluster labels. |
148 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
148 |
+#' @param altExpName The name for the \link{altExp} slot |
|
149 | 149 |
#' to use. Default "featureSubset". |
150 | 150 |
#' @return \linkS4class{SingleCellExperiment} object with recoded cell |
151 | 151 |
#' cluster labels. |
... | ... |
@@ -188,13 +188,13 @@ recodeClusterZ <- function(sce, from, to, altExpName = "featureSubset") { |
188 | 188 |
#' @param sce \linkS4class{SingleCellExperiment} object returned from |
189 | 189 |
#' \link{celda_G} or \link{celda_CG}. Must contain column |
190 | 190 |
#' \code{celda_feature_module} in |
191 |
-#' \code{\link[SummarizedExperiment]{rowData}(altExp(sce, altExpName))}. |
|
191 |
+#' \code{\link{rowData}(altExp(sce, altExpName))}. |
|
192 | 192 |
#' @param from Numeric vector. Unique values in the range of |
193 | 193 |
#' \code{seq(celdaModules(sce))} that correspond to the original module labels |
194 | 194 |
#' in \code{sce}. |
195 | 195 |
#' @param to Numeric vector. Unique values in the range of |
196 | 196 |
#' \code{seq(celdaModules(sce))} that correspond to the new module labels. |
197 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
197 |
+#' @param altExpName The name for the \link{altExp} slot |
|
198 | 198 |
#' to use. Default "featureSubset". |
199 | 199 |
#' @return @return \linkS4class{SingleCellExperiment} object with recoded |
200 | 200 |
#' feature module labels. |
... | ... |
@@ -525,9 +525,9 @@ distinctColors <- function(n, |
525 | 525 |
#' \link{celda_G}, or \link{celda_CG}, with the matrix |
526 | 526 |
#' located in the \code{useAssay} assay slot. |
527 | 527 |
#' Rows represent features and columns represent cells. |
528 |
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} |
|
528 |
+#' @param useAssay A string specifying which \link{assay} |
|
529 | 529 |
#' slot to use. Default "counts". |
530 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
530 |
+#' @param altExpName The name for the \link{altExp} slot |
|
531 | 531 |
#' to use. Default "featureSubset". |
532 | 532 |
#' @param outputFile File name for feature module table. If NULL, file will |
533 | 533 |
#' not be created. Default NULL. |
... | ... |
@@ -3,9 +3,9 @@ |
3 | 3 |
#' clustering results. |
4 | 4 |
#' @param sce A \link[SingleCellExperiment]{SingleCellExperiment} object |
5 | 5 |
#' returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}. |
6 |
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} |
|
6 |
+#' @param useAssay A string specifying which \link{assay} |
|
7 | 7 |
#' slot to use. Default "counts". |
8 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
8 |
+#' @param altExpName The name for the \link{altExp} slot |
|
9 | 9 |
#' to use. Default "featureSubset". |
10 | 10 |
#' @param featureIx Integer vector. Select features for display in heatmap. If |
11 | 11 |
#' NULL, no subsetting will be performed. Default NULL. \strong{Only used for |
... | ... |
@@ -8,9 +8,9 @@ |
8 | 8 |
#' Module probabilities are square-root transformed before applying tSNE. |
9 | 9 |
#' @param sce A \linkS4class{SingleCellExperiment} object |
10 | 10 |
#' returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}. |
11 |
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} |
|
11 |
+#' @param useAssay A string specifying which \link{assay} |
|
12 | 12 |
#' slot to use. Default "counts". |
13 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
13 |
+#' @param altExpName The name for the \link{altExp} slot |
|
14 | 14 |
#' to use. Default "featureSubset". |
15 | 15 |
#' @param maxCells Integer. Maximum number of cells to plot. Cells will be |
16 | 16 |
#' randomly subsampled if \code{ncol(counts) > maxCells}. Larger numbers of |
... | ... |
@@ -48,7 +48,7 @@ |
48 | 48 |
#' @param ... Ignored. Placeholder to prevent check warning. |
49 | 49 |
#' @return \code{sce} with t-SNE coordinates |
50 | 50 |
#' (columns "celda_tSNE1" & "celda_tSNE2") added to |
51 |
-#' \code{\link[SingleCellExperiment]{reducedDim}(sce, "celda_tSNE")}. |
|
51 |
+#' \code{\link{reducedDim}(sce, "celda_tSNE")}. |
|
52 | 52 |
#' @export |
53 | 53 |
setGeneric("celdaTsne", |
54 | 54 |
function(sce, ...) { |
... | ... |
@@ -11,17 +11,17 @@ |
11 | 11 |
#' \code{celdaModel}. Dimensions and MD5 checksum will be checked by |
12 | 12 |
#' \link{compareCountMatrix}. |
13 | 13 |
#' @param useAssay A string specifying the name of the |
14 |
-#' \link[SummarizedExperiment]{assay} slot to use. Default "counts". |
|
15 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
14 |
+#' \link{assay} slot to use. Default "counts". |
|
15 |
+#' @param altExpName The name for the \link{altExp} slot |
|
16 | 16 |
#' to use. Default "featureSubset". |
17 | 17 |
#' @param ... Ignored. Placeholder to prevent check warning. |
18 | 18 |
#' @return A \linkS4class{SingleCellExperiment} object. Function |
19 |
-#' parameter settings are stored in the \link[S4Vectors]{metadata} |
|
19 |
+#' parameter settings are stored in the \link{metadata} |
|
20 | 20 |
#' \code{"celda_parameters"} slot. |
21 | 21 |
#' Columns \code{celda_sample_label} and \code{celda_cell_cluster} in |
22 |
-#' \link[SummarizedExperiment]{colData} contain sample labels and celda cell |
|
22 |
+#' \link{colData} contain sample labels and celda cell |
|
23 | 23 |
#' population clusters. Column \code{celda_feature_module} in |
24 |
-#' \link[SummarizedExperiment]{rowData} contain feature modules. |
|
24 |
+#' \link{rowData} contain feature modules. |
|
25 | 25 |
#' @export |
26 | 26 |
setGeneric("celdatosce", function(celdaModel, counts, ...) { |
27 | 27 |
standardGeneric("celdatosce")}) |
... | ... |
@@ -8,9 +8,9 @@ |
8 | 8 |
#' \link{celda_C}, \link{celda_G}, or \link{celda_CG}, with the matrix |
9 | 9 |
#' located in the \code{useAssay} assay slot. |
10 | 10 |
#' Rows represent features and columns represent cells. |
11 |
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} |
|
11 |
+#' @param useAssay A string specifying which \link{assay} |
|
12 | 12 |
#' slot to use. Default "counts". |
13 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
13 |
+#' @param altExpName The name for the \link{altExp} slot |
|
14 | 14 |
#' to use. Default "featureSubset". |
15 | 15 |
#' @param log Logical. If \code{FALSE}, then the normalized conditional |
16 | 16 |
#' probabilities will be returned. If \code{TRUE}, then the unnormalized log |
... | ... |
@@ -7,10 +7,10 @@ |
7 | 7 |
#' Rows represent features and columns represent cells. Must contain cluster |
8 | 8 |
#' labels in \code{celdaClusters(x, altExpName = altExpName)} if \code{x} is a |
9 | 9 |
#' \linkS4class{SingleCellExperiment} object. |
10 |
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} |
|
10 |
+#' @param useAssay A string specifying which \link{assay} |
|
11 | 11 |
#' slot to use if \code{x} is a |
12 | 12 |
#' \link[SingleCellExperiment]{SingleCellExperiment} object. Default "counts". |
13 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
13 |
+#' @param altExpName The name for the \link{altExp} slot |
|
14 | 14 |
#' to use. Default "featureSubset". |
15 | 15 |
#' @param celdaMod Celda object of class `celda_C` or `celda_CG`. |
16 | 16 |
#' @param c1 Integer vector. Cell populations to include in group 1 for the |
... | ... |
@@ -11,10 +11,10 @@ |
11 | 11 |
#' \item Integer counts matrix. Rows represent features and columns represent |
12 | 12 |
#' cells. This matrix should be the same as the one used to generate |
13 | 13 |
#' \code{celdaMod}.} |
14 |
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} |
|
14 |
+#' @param useAssay A string specifying which \link{assay} |
|
15 | 15 |
#' slot to use if \code{x} is a \linkS4class{SingleCellExperiment} object. |
16 | 16 |
#' Default "counts". |
17 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
17 |
+#' @param altExpName The name for the \link{altExp} slot |
|
18 | 18 |
#' to use. Default "featureSubset". |
19 | 19 |
#' @param celdaMod Celda model object. Only works if \code{x} is an integer |
20 | 20 |
#' counts matrix. |
... | ... |
@@ -8,7 +8,7 @@ |
8 | 8 |
#' Rows represent features and columns represent cells. |
9 | 9 |
#' @param feature Character vector. Identify feature modules for the specified |
10 | 10 |
#' feature names. \code{feature} must match the rownames of \code{sce}. |
11 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
11 |
+#' @param altExpName The name for the \link{altExp} slot |
|
12 | 12 |
#' to use. Default "featureSubset". |
13 | 13 |
#' @param exactMatch Logical. Whether to look for exactMatch of the gene name |
14 | 14 |
#' within counts matrix. Default \code{TRUE}. |
... | ... |
@@ -9,10 +9,10 @@ |
9 | 9 |
#' \linkS4class{SingleCellExperiment} |
10 | 10 |
#' with the matrix located in the assay slot under \code{useAssay}. |
11 | 11 |
#' Rows represent features and columns represent cells. |
12 |
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} |
|
12 |
+#' @param useAssay A string specifying which \link{assay} |
|
13 | 13 |
#' slot to use if \code{x} is a |
14 | 14 |
#' \link[SingleCellExperiment]{SingleCellExperiment} object. Default "counts". |
15 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
15 |
+#' @param altExpName The name for the \link{altExp} slot |
|
16 | 16 |
#' to use. Default "featureSubset". |
17 | 17 |
#' @param class Vector of cell cluster labels. |
18 | 18 |
#' @param oneoffMetric A character string. What one-off metric to run, either |
... | ... |
@@ -9,10 +9,10 @@ |
9 | 9 |
#' with the matrix located in the assay slot under \code{useAssay}. |
10 | 10 |
#' Rows represent features and columns represent cells. Rownames of the |
11 | 11 |
#' matrix or \linkS4class{SingleCellExperiment} object should be gene names. |
12 |
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} |
|
12 |
+#' @param useAssay A string specifying which \link{assay} |
|
13 | 13 |
#' slot to use if \code{x} is a |
14 | 14 |
#' \linkS4class{SingleCellExperiment} object. Default "counts". |
15 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
15 |
+#' @param altExpName The name for the \link{altExp} slot |
|
16 | 16 |
#' to use. Default "featureSubset". |
17 | 17 |
#' @param celdaModel Celda object of class \code{celda_G} or \code{celda_CG}. |
18 | 18 |
#' @param databases Character vector. Name of reference database. Available |
... | ... |
@@ -5,9 +5,9 @@ |
5 | 5 |
#' \link{celda_C}, \link{celda_G}, or \link{celda_CG}, with the matrix |
6 | 6 |
#' located in the \code{useAssay} assay slot. |
7 | 7 |
#' Rows represent features and columns represent cells. |
8 |
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} |
|
8 |
+#' @param useAssay A string specifying which \link{assay} |
|
9 | 9 |
#' slot to use. Default "counts". |
10 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
10 |
+#' @param altExpName The name for the \link{altExp} slot |
|
11 | 11 |
#' to use. Default "featureSubset". |
12 | 12 |
#' @param celdaMod celda model object. Ignored if \code{x} is a |
13 | 13 |
#' \linkS4class{SingleCellExperiment} object. |
... | ... |
@@ -154,7 +154,7 @@ setMethod("logLikelihood", signature(x = "matrix", celdaMod = "celda_CG"), |
154 | 154 |
#' @param x A \linkS4class{SingleCellExperiment} object |
155 | 155 |
#' returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}, or a celda |
156 | 156 |
#' model object. |
157 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
157 |
+#' @param altExpName The name for the \link{altExp} slot |
|
158 | 158 |
#' to use. Default "featureSubset". |
159 | 159 |
#' @param ... Ignored. Placeholder to prevent check warning. |
160 | 160 |
#' @return Numeric. The log-likelihood at each step of Gibbs sampling used to |
... | ... |
@@ -205,7 +205,7 @@ setMethod("logLikelihoodHistory", |
205 | 205 |
#' @param x A \linkS4class{SingleCellExperiment} object |
206 | 206 |
#' returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}, or a celda |
207 | 207 |
#' model object. |
208 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
208 |
+#' @param altExpName The name for the \link{altExp} slot |
|
209 | 209 |
#' to use. Default "featureSubset". |
210 | 210 |
#' @param ... Ignored. Placeholder to prevent check warning. |
211 | 211 |
#' @export |
... | ... |
@@ -10,10 +10,10 @@ |
10 | 10 |
#' \linkS4class{SingleCellExperiment} |
11 | 11 |
#' with the matrix located in the assay slot under \code{useAssay}. |
12 | 12 |
#' Rows represent features and columns represent cells. |
13 |
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} |
|
13 |
+#' @param useAssay A string specifying which \link{assay} |
|
14 | 14 |
#' slot to use if \code{x} is a |
15 | 15 |
#' \linkS4class{SingleCellExperiment} object. Default "counts". |
16 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
16 |
+#' @param altExpName The name for the \link{altExp} slot |
|
17 | 17 |
#' to use. Default "featureSubset". |
18 | 18 |
#' @param featureModule Integer Vector. The featureModule(s) to display. |
19 | 19 |
#' Multiple modules can be included in a vector. Default \code{NULL} which |
... | ... |
@@ -10,10 +10,10 @@ |
10 | 10 |
#' \item Integer counts matrix. Rows represent features and columns represent |
11 | 11 |
#' cells. This matrix should be the same as the one used to generate |
12 | 12 |
#' \code{celdaMod}.} |
13 |
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} |
|
13 |
+#' @param useAssay A string specifying which \link{assay} |
|
14 | 14 |
#' slot to use if \code{x} is a \linkS4class{SingleCellExperiment} object. |
15 | 15 |
#' Default "counts". |
16 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
16 |
+#' @param altExpName The name for the \link{altExp} slot |
|
17 | 17 |
#' to use. Default "featureSubset". |
18 | 18 |
#' @param celdaMod Celda model object. Only works if \code{x} is an integer |
19 | 19 |
#' counts matrix. |
... | ... |
@@ -347,10 +347,10 @@ setMethod( |
347 | 347 |
#' Rows represent features and columns represent cells. Must contain |
348 | 348 |
#' "celda_grid_search" slot in \code{metadata(x)} if \code{x} is a |
349 | 349 |
#' \linkS4class{SingleCellExperiment} object. |
350 |
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} |
|
350 |
+#' @param useAssay A string specifying which \link{assay} |
|
351 | 351 |
#' slot to use if \code{x} is a |
352 | 352 |
#' \linkS4class{SingleCellExperiment} object. Default "counts". |
353 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
353 |
+#' @param altExpName The name for the \link{altExp} slot |
|
354 | 354 |
#' to use. Default "featureSubset". |
355 | 355 |
#' @param celdaList Object of class 'celdaList'. Used only if \code{x} is a |
356 | 356 |
#' matrix object. |
... | ... |
@@ -483,7 +483,7 @@ setMethod("resamplePerplexity", |
483 | 483 |
#' or \code{recursiveSplitCell}. Must contain a list named |
484 | 484 |
#' \code{"celda_grid_search"} in \code{metadata(x)}. |
485 | 485 |
#' \item celdaList object.} |
486 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
486 |
+#' @param altExpName The name for the \link{altExp} slot |
|
487 | 487 |
#' to use. Default "featureSubset". |
488 | 488 |
#' @param sep Numeric. Breaks in the x axis of the resulting plot. |
489 | 489 |
#' @param ... Ignored. Placeholder to prevent check warning. |
... | ... |
@@ -743,7 +743,7 @@ setMethod("plotGridSearchPerplexity", |
743 | 743 |
#' or \code{recursiveSplitCell}. Must contain a list named |
744 | 744 |
#' \code{"celda_grid_search"} in \code{metadata(x)}. |
745 | 745 |
#' \item celdaList object.} |
746 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
746 |
+#' @param altExpName The name for the \link{altExp} slot |
|
747 | 747 |
#' to use. Default "featureSubset". |
748 | 748 |
#' @param sep Numeric. Breaks in the x axis of the resulting plot. |
749 | 749 |
#' @param n Integer. Width of the rolling window. Default 10. |
... | ... |
@@ -12,15 +12,15 @@ |
12 | 12 |
#' reduction output. |
13 | 13 |
#' @param dim2 Numeric vector. Second dimension from data dimension |
14 | 14 |
#' reduction output. |
15 |
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} |
|
15 |
+#' @param useAssay A string specifying which \link{assay} |
|
16 | 16 |
#' slot to use if \code{x} is a |
17 | 17 |
#' \linkS4class{SingleCellExperiment} object. Default "counts". |
18 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
18 |
+#' @param altExpName The name for the \link{altExp} slot |
|
19 | 19 |
#' to use. Default "featureSubset". |
20 | 20 |
#' @param size Numeric. Sets size of point on plot. Default 1. |
21 | 21 |
#' @param xlab Character vector. Label for the x-axis. Default 'Dimension_1'. |
22 | 22 |
#' @param ylab Character vector. Label for the y-axis. Default 'Dimension_2'. |
23 |
-#' @param limits Passed to \link[ggplot2]{scale_colour_gradient2}. The range |
|
23 |
+#' @param limits Passed to \link{scale_colour_gradient2}. The range |
|
24 | 24 |
#' of color scale. |
25 | 25 |
#' @param colorLow Character. A color available from `colors()`. |
26 | 26 |
#' The color will be used to signify the lowest values on the scale. |
... | ... |
@@ -291,10 +291,10 @@ setMethod("plotDimReduceGrid", |
291 | 291 |
#' dimension reduction output. |
292 | 292 |
#' @param dim2 Numeric vector. Second dimension from data dimension |
293 | 293 |
#' reduction output. |
294 |
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} |
|
294 |
+#' @param useAssay A string specifying which \link{assay} |
|
295 | 295 |
#' slot to use if \code{x} is a |
296 | 296 |
#' \linkS4class{SingleCellExperiment} object. Default "counts". |
297 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
297 |
+#' @param altExpName The name for the \link{altExp} slot |
|
298 | 298 |
#' to use. Default "featureSubset". |
299 | 299 |
#' @param features Character vector. Features in the rownames of counts to plot. |
300 | 300 |
#' @param headers Character vector. If `NULL`, the corresponding rownames are |
... | ... |
@@ -309,7 +309,7 @@ setMethod("plotDimReduceGrid", |
309 | 309 |
#' @param trim Numeric vector. Vector of length two that specifies the lower |
310 | 310 |
#' and upper bounds for the data. This threshold is applied after row scaling. |
311 | 311 |
#' Set to NULL to disable. Default \code{c(-1,1)}. |
312 |
-#' @param limits Passed to \link[ggplot2]{scale_colour_gradient2}. The range |
|
312 |
+#' @param limits Passed to \link{scale_colour_gradient2}. The range |
|
313 | 313 |
#' of color scale. |
314 | 314 |
#' @param size Numeric. Sets size of point on plot. Default 1. |
315 | 315 |
#' @param xlab Character vector. Label for the x-axis. Default "Dimension_1". |
... | ... |
@@ -576,10 +576,10 @@ setMethod("plotDimReduceFeature", |
576 | 576 |
#' First dimension from data dimension reduction output. |
577 | 577 |
#' @param dim2 Numeric vector. |
578 | 578 |
#' Second dimension from data dimension reduction output. |
579 |
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} |
|
579 |
+#' @param useAssay A string specifying which \link{assay} |
|
580 | 580 |
#' slot to use if \code{x} is a |
581 | 581 |
#' \linkS4class{SingleCellExperiment} object. Default "counts". |
582 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
582 |
+#' @param altExpName The name for the \link{altExp} slot |
|
583 | 583 |
#' to use. Default "featureSubset". |
584 | 584 |
#' @param celdaMod Celda object of class "celda_G" or "celda_CG". Used only if |
585 | 585 |
#' \code{x} is a matrix object. |
... | ... |
@@ -587,7 +587,7 @@ setMethod("plotDimReduceFeature", |
587 | 587 |
#' e.g. c("1", "2"). |
588 | 588 |
#' @param rescale Logical. |
589 | 589 |
#' Whether rows of the matrix should be rescaled to [0, 1]. Default TRUE. |
590 |
-#' @param limits Passed to \link[ggplot2]{scale_colour_gradient}. The range |
|
590 |
+#' @param limits Passed to \link{scale_colour_gradient}. The range |
|
591 | 591 |
#' of color scale. |
592 | 592 |
#' @param size Numeric. Sets size of point on plot. Default 1. |
593 | 593 |
#' @param xlab Character vector. Label for the x-axis. Default "Dimension_1". |
... | ... |
@@ -814,7 +814,7 @@ setMethod("plotDimReduceModule", |
814 | 814 |
#' \code{reducedDimNames(x)} if \code{x} is a |
815 | 815 |
#' \linkS4class{SingleCellExperiment} object. Ignored if both \code{dim1} and |
816 | 816 |
#' \code{dim2} are set. |
817 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
817 |
+#' @param altExpName The name for the \link{altExp} slot |
|
818 | 818 |
#' to use. Default "featureSubset". |
819 | 819 |
#' @param dim1 Numeric vector. First dimension from data |
820 | 820 |
#' dimension reduction output. |
... | ... |
@@ -1027,10 +1027,10 @@ setMethod("plotDimReduceCluster", |
1027 | 1027 |
#' with the matrix located in the assay slot under \code{useAssay}. Rows |
1028 | 1028 |
#' represent features and columns represent cells. |
1029 | 1029 |
#' @param features Character vector. Uses these genes for plotting. |
1030 |
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} |
|
1030 |
+#' @param useAssay A string specifying which \link{assay} |
|
1031 | 1031 |
#' slot to use if \code{x} is a |
1032 | 1032 |
#' \linkS4class{SingleCellExperiment} object. Default "counts". |
1033 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
1033 |
+#' @param altExpName The name for the \link{altExp} slot |
|
1034 | 1034 |
#' to use. Default "featureSubset". |
1035 | 1035 |
#' @param celdaMod Celda object of class "celda_G" or "celda_CG". Used only if |
1036 | 1036 |
#' \code{x} is a matrix object. |
... | ... |
@@ -90,9 +90,9 @@ |
90 | 90 |
#' with the matrix located in the assay slot under \code{useAssay}. |
91 | 91 |
#' Rows represent features and columns represent cells. |
92 | 92 |
#' @param useAssay A string specifying the name of the |
93 |
-#' \link[SummarizedExperiment]{assay} |
|
93 |
+#' \link{assay} |
|
94 | 94 |
#' slot to use. Default "counts". |
95 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
95 |
+#' @param altExpName The name for the \link{altExp} slot |
|
96 | 96 |
#' to use. Default "featureSubset". |
97 | 97 |
#' @param sampleLabel Vector or factor. Denotes the sample label for each cell |
98 | 98 |
#' (column) in the count matrix. |
... | ... |
@@ -137,7 +137,7 @@ |
137 | 137 |
#' @param ... Ignored. Placeholder to prevent check warning. |
138 | 138 |
#' @return A \linkS4class{SingleCellExperiment} object. Function |
139 | 139 |
#' parameter settings and celda model results are stored in the |
140 |
-#' \link[S4Vectors]{metadata} \code{"celda_grid_search"} slot. The models in |
|
140 |
+#' \link{metadata} \code{"celda_grid_search"} slot. The models in |
|
141 | 141 |
#' the list will be of class \code{celda_C} if \code{yInit = NULL} or |
142 | 142 |
#' \code{celda_CG} if \code{zInit} is set. |
143 | 143 |
#' @seealso \link{recursiveSplitModule} for recursive splitting of feature |
... | ... |
@@ -859,10 +859,10 @@ setMethod("recursiveSplitCell", |
859 | 859 |
#' \linkS4class{SingleCellExperiment} |
860 | 860 |
#' with the matrix located in the assay slot under \code{useAssay}. |
861 | 861 |
#' Rows represent features and columns represent cells. |
862 |
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} |
|
862 |
+#' @param useAssay A string specifying which \link{assay} |
|
863 | 863 |
#' slot to use if \code{x} is a |
864 | 864 |
#' \link[SingleCellExperiment]{SingleCellExperiment} object. Default "counts". |
865 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
865 |
+#' @param altExpName The name for the \link{altExp} slot |
|
866 | 866 |
#' to use. Default "featureSubset". |
867 | 867 |
#' @param initialL Integer. Minimum number of modules to try. |
868 | 868 |
#' @param maxL Integer. Maximum number of modules to try. |
... | ... |
@@ -905,7 +905,7 @@ setMethod("recursiveSplitCell", |
905 | 905 |
#' @param ... Ignored. Placeholder to prevent check warning. |
906 | 906 |
#' @return A \linkS4class{SingleCellExperiment} object. Function |
907 | 907 |
#' parameter settings and celda model results are stored in the |
908 |
-#' \link[S4Vectors]{metadata} \code{"celda_grid_search"} slot. The models in |
|
908 |
+#' \link{metadata} \code{"celda_grid_search"} slot. The models in |
|
909 | 909 |
#' the list will be of class \link{celda_G} if \code{zInit = NULL} or |
910 | 910 |
#' \link{celda_CG} if \code{zInit} is set. |
911 | 911 |
#' @seealso \code{recursiveSplitCell} for recursive splitting of cell |
... | ... |
@@ -3,8 +3,8 @@ |
3 | 3 |
#' Select features with at least \code{minCount} counts |
4 | 4 |
#' in at least \code{minCell} cells. A \linkS4class{SingleCellExperiment} |
5 | 5 |
#' object with subset features will be stored in the |
6 |
-#' \link[SingleCellExperiment]{altExp} slot with name \code{altExpName}. |
|
7 |
-#' The name of the \code{assay} slot in \link[SingleCellExperiment]{altExp} |
|
6 |
+#' \link{altExp} slot with name \code{altExpName}. |
|
7 |
+#' The name of the \code{assay} slot in \link{altExp} |
|
8 | 8 |
#' will be the same as \code{useAssay}. |
9 | 9 |
#' @param x A numeric \link{matrix} of counts or a |
10 | 10 |
#' \linkS4class{SingleCellExperiment} |
... | ... |
@@ -13,13 +13,13 @@ |
13 | 13 |
#' @param minCount Minimum number of counts required for feature selection. |
14 | 14 |
#' @param minCell Minimum number of cells required for feature selection. |
15 | 15 |
#' @param useAssay A string specifying the name of the |
16 |
-#' \link[SummarizedExperiment]{assay} slot to use. Default "counts". |
|
17 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
16 |
+#' \link{assay} slot to use. Default "counts". |
|
17 |
+#' @param altExpName The name for the \link{altExp} slot |
|
18 | 18 |
#' to use. Default "featureSubset". |
19 | 19 |
#' @param ... Ignored. Placeholder to prevent check warning. |
20 | 20 |
#' @return A \linkS4class{SingleCellExperiment} object with a |
21 |
-#' \code{altExpName} \link[SingleCellExperiment]{altExp} slot. Function |
|
22 |
-#' parameter settings are stored in the \link[S4Vectors]{metadata} |
|
21 |
+#' \code{altExpName} \link{altExp} slot. Function |
|
22 |
+#' parameter settings are stored in the \link{metadata} |
|
23 | 23 |
#' \code{"select_features"} slot. |
24 | 24 |
#' @export |
25 | 25 |
setGeneric("selectFeatures", function(x, ...) { |
... | ... |
@@ -41,13 +41,13 @@ |
41 | 41 |
#' \link[withr]{with_seed} are made. |
42 | 42 |
#' @return A \link[SingleCellExperiment]{SingleCellExperiment} object with |
43 | 43 |
#' simulated count matrix stored in the "counts" assay slot. Function |
44 |
-#' parameter settings are stored in the \link[S4Vectors]{metadata} slot. For |
|
44 |
+#' parameter settings are stored in the \link{metadata} slot. For |
|
45 | 45 |
#' \code{"celda_CG"} and \code{"celda_C"} models, |
46 | 46 |
#' columns \code{celda_sample_label} and \code{celda_cell_cluster} in |
47 |
-#' \link[SummarizedExperiment]{colData} contain simulated sample labels and |
|
47 |
+#' \link{colData} contain simulated sample labels and |
|
48 | 48 |
#' cell population clusters. For \code{"celda_CG"} and \code{"celda_G"} |
49 | 49 |
#' models, column \code{celda_feature_module} in |
50 |
-#' \link[SummarizedExperiment]{rowData} contains simulated gene modules. |
|
50 |
+#' \link{rowData} contains simulated gene modules. |
|
51 | 51 |
#' @examples |
52 | 52 |
#' sce <- simulateCells() |
53 | 53 |
#' @export |
... | ... |
@@ -5,9 +5,9 @@ |
5 | 5 |
#' @param x A \linkS4class{SingleCellExperiment} object |
6 | 6 |
#' with the matrix located in the assay slot under \code{useAssay}. |
7 | 7 |
#' Rows represent features and columns represent cells. |
8 |
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} |
|
8 |
+#' @param useAssay A string specifying which \link{assay} |
|
9 | 9 |
#' slot to use for \code{x}. Default "counts". |
10 |
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot |
|
10 |
+#' @param altExpName The name for the \link{altExp} slot |
|
11 | 11 |
#' to use. Default "featureSubset". |
12 | 12 |
#' @param module Integer. The module to be split. |
13 | 13 |
#' @param n Integer. How many modules should \code{module} be split into. |
... | ... |
@@ -18,7 +18,7 @@ |
18 | 18 |
#' @param ... Ignored. Placeholder to prevent check warning. |
19 | 19 |
#' @return A updated \linkS4class{SingleCellExperiment} object with new |
20 | 20 |
#' feature modules stored in column \code{celda_feature_module} in |
21 |
-#' \code{\link[SummarizedExperiment]{rowData}(x)}. |
|
21 |
+#' \code{\link{rowData}(x)}. |
|
22 | 22 |
#' @export |
23 | 23 |
setGeneric("splitModule", |
24 | 24 |
function(x, ...) { |
... | ... |
@@ -19,7 +19,7 @@ model object.} |
19 | 19 |
|
20 | 20 |
\item{...}{Ignored. Placeholder to prevent check warning.} |
21 | 21 |
|
22 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
22 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
23 | 23 |
to use. Default "featureSubset".} |
24 | 24 |
} |
25 | 25 |
\value{ |
... | ... |
@@ -26,13 +26,13 @@ celdaClusters(x, altExpName = "featureSubset") <- value |
26 | 26 |
\item A \linkS4class{SingleCellExperiment} object returned by |
27 | 27 |
\link{celda_C}, or \link{celda_CG}, with the matrix |
28 | 28 |
located in the \code{useAssay} assay slot. The |
29 |
-a \link[SingleCellExperiment]{altExp} slot with name \code{altExpName} will |
|
29 |
+a \link{altExp} slot with name \code{altExpName} will |
|
30 | 30 |
be used. Rows represent features and columns represent cells. |
31 | 31 |
\item Celda model object.}} |
32 | 32 |
|
33 | 33 |
\item{...}{Ignored. Placeholder to prevent check warning.} |
34 | 34 |
|
35 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
35 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
36 | 36 |
to use. Default "featureSubset".} |
37 | 37 |
|
38 | 38 |
\item{value}{Character vector of cell cluster labels for replacements. Works |
... | ... |
@@ -51,9 +51,9 @@ Rows represent features and columns represent cells.} |
51 | 51 |
\item{...}{Ignored. Placeholder to prevent check warning.} |
52 | 52 |
|
53 | 53 |
\item{useAssay}{A string specifying the name of the |
54 |
-\link[SummarizedExperiment]{assay} slot to use. Default "counts".} |
|
54 |
+\link{assay} slot to use. Default "counts".} |
|
55 | 55 |
|
56 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
56 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
57 | 57 |
to use. Default "featureSubset".} |
58 | 58 |
|
59 | 59 |
\item{model}{Celda model. Options available in \link{availableModels}.} |
... | ... |
@@ -98,7 +98,7 @@ and main process. Default "Celda".} |
98 | 98 |
\value{ |
99 | 99 |
A \linkS4class{SingleCellExperiment} object. Function |
100 | 100 |
parameter settings and celda model results are stored in the |
101 |
- \link[S4Vectors]{metadata} \code{"celda_grid_search"} slot. |
|
101 |
+ \link{metadata} \code{"celda_grid_search"} slot. |
|
102 | 102 |
} |
103 | 103 |
\description{ |
104 | 104 |
Run Celda with different combinations of parameters and |
... | ... |
@@ -22,10 +22,10 @@ returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.} |
22 | 22 |
|
23 | 23 |
\item{...}{Additional parameters passed to \link{plotHeatmap}.} |
24 | 24 |
|
25 |
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} |
|
25 |
+\item{useAssay}{A string specifying which \link{assay} |
|
26 | 26 |
slot to use. Default "counts".} |
27 | 27 |
|
28 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
28 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
29 | 29 |
to use. Default "featureSubset".} |
30 | 30 |
|
31 | 31 |
\item{featureIx}{Integer vector. Select features for display in heatmap. If |
... | ... |
@@ -16,7 +16,7 @@ returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.} |
16 | 16 |
|
17 | 17 |
\item{...}{Ignored. Placeholder to prevent check warning.} |
18 | 18 |
|
19 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
19 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
20 | 20 |
to use. Default "featureSubset".} |
21 | 21 |
} |
22 | 22 |
\value{ |
... | ... |
@@ -22,7 +22,7 @@ celdaModules(sce, altExpName = "featureSubset") <- value |
22 | 22 |
located in the \code{useAssay} assay slot. |
23 | 23 |
Rows represent features and columns represent cells.} |
24 | 24 |
|
25 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
25 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
26 | 26 |
to use. Default "featureSubset".} |
27 | 27 |
|
28 | 28 |
\item{value}{Character vector of feature module labels for replacements. |
... | ... |
@@ -32,10 +32,10 @@ returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.} |
32 | 32 |
|
33 | 33 |
\item{...}{Additional parameters passed to \link[ComplexHeatmap]{Heatmap}.} |
34 | 34 |
|
35 |
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} |
|
35 |
+\item{useAssay}{A string specifying which \link{assay} |
|
36 | 36 |
slot to use. Default "counts".} |
37 | 37 |
|
38 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
38 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
39 | 39 |
to use. Default "featureSubset".} |
40 | 40 |
|
41 | 41 |
\item{level}{Character. One of "cellPopulation" or "Sample". |
... | ... |
@@ -30,10 +30,10 @@ returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.} |
30 | 30 |
|
31 | 31 |
\item{...}{Ignored. Placeholder to prevent check warning.} |
32 | 32 |
|
33 |
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} |
|
33 |
+\item{useAssay}{A string specifying which \link{assay} |
|
34 | 34 |
slot to use. Default "counts".} |
35 | 35 |
|
36 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
36 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
37 | 37 |
to use. Default "featureSubset".} |
38 | 38 |
|
39 | 39 |
\item{maxCells}{Integer. Maximum number of cells to plot. Cells will be |
... | ... |
@@ -82,7 +82,7 @@ a default value of 12345 is used. If NULL, no calls to |
82 | 82 |
\value{ |
83 | 83 |
\code{sce} with t-SNE coordinates |
84 | 84 |
(columns "celda_tSNE1" & "celda_tSNE2") added to |
85 |
- \code{\link[SingleCellExperiment]{reducedDim}(sce, "celda_tSNE")}. |
|
85 |
+ \code{\link{reducedDim}(sce, "celda_tSNE")}. |
|
86 | 86 |
} |
87 | 87 |
\description{ |
88 | 88 |
Embeds cells in two dimensions using \link[Rtsne]{Rtsne} based |
... | ... |
@@ -34,10 +34,10 @@ returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.} |
34 | 34 |
|
35 | 35 |
\item{...}{Additional parameters to pass to \link[uwot]{umap}.} |
36 | 36 |
|
37 |
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} |
|
37 |
+\item{useAssay}{A string specifying which \link{assay} |
|
38 | 38 |
slot to use. Default "counts".} |
39 | 39 |
|
40 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
40 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
41 | 41 |
to use. Default "featureSubset".} |
42 | 42 |
|
43 | 43 |
\item{maxCells}{Integer. Maximum number of cells to plot. Cells will be |
... | ... |
@@ -103,7 +103,7 @@ be applied. Occurs after applying normalization and scale factor. Default |
103 | 103 |
\value{ |
104 | 104 |
\code{sce} with UMAP coordinates |
105 | 105 |
(columns "celda_UMAP1" & "celda_UMAP2") added to |
106 |
- \code{\link[SingleCellExperiment]{reducedDim}(sce, "celda_UMAP")}. |
|
106 |
+ \code{\link{reducedDim}(sce, "celda_UMAP")}. |
|
107 | 107 |
} |
108 | 108 |
\description{ |
109 | 109 |
Embeds cells in two dimensions using \link[uwot]{umap} based on |
... | ... |
@@ -62,9 +62,9 @@ Rows represent features and columns represent cells.} |
62 | 62 |
\item{...}{Ignored. Placeholder to prevent check warning.} |
63 | 63 |
|
64 | 64 |
\item{useAssay}{A string specifying the name of the |
65 |
-\link[SummarizedExperiment]{assay} slot to use. Default "counts".} |
|
65 |
+\link{assay} slot to use. Default "counts".} |
|
66 | 66 |
|
67 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
67 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
68 | 68 |
to use. Default "featureSubset".} |
69 | 69 |
|
70 | 70 |
\item{sampleLabel}{Vector or factor. Denotes the sample label for each cell |
... | ... |
@@ -127,19 +127,19 @@ can only be used when `initialize = 'random'`. Default NULL.} |
127 | 127 |
} |
128 | 128 |
\value{ |
129 | 129 |
A \link[SingleCellExperiment]{SingleCellExperiment} object. Function |
130 |
- parameter settings are stored in the \link[S4Vectors]{metadata} |
|
130 |
+ parameter settings are stored in the \link{metadata} |
|
131 | 131 |
\code{"celda_parameters"} slot. |
132 | 132 |
Columns \code{celda_sample_label} and \code{celda_cell_cluster} in |
133 |
- \link[SummarizedExperiment]{colData} contain sample labels and celda cell |
|
133 |
+ \link{colData} contain sample labels and celda cell |
|
134 | 134 |
population clusters. |
135 | 135 |
} |
136 | 136 |
\description{ |
137 | 137 |
Clusters the columns of a count matrix containing single-cell |
138 | 138 |
data into K subpopulations. The |
139 |
- \code{useAssay} \link[SummarizedExperiment]{assay} slot in |
|
140 |
- \code{altExpName} \link[SingleCellExperiment]{altExp} slot will be used if |
|
139 |
+ \code{useAssay} \link{assay} slot in |
|
140 |
+ \code{altExpName} \link{altExp} slot will be used if |
|
141 | 141 |
it exists. Otherwise, the \code{useAssay} |
142 |
- \link[SummarizedExperiment]{assay} slot in \code{x} will be used if |
|
142 |
+ \link{assay} slot in \code{x} will be used if |
|
143 | 143 |
\code{x} is a \linkS4class{SingleCellExperiment} object. |
144 | 144 |
} |
145 | 145 |
\examples{ |
... | ... |
@@ -65,16 +65,16 @@ celda_CG(x, ...) |
65 | 65 |
\arguments{ |
66 | 66 |
\item{x}{A numeric \link{matrix} of counts or a |
67 | 67 |
\linkS4class{SingleCellExperiment} |
68 |
-with the matrix located in the \link[SummarizedExperiment]{assay} |
|
68 |
+with the matrix located in the \link{assay} |
|
69 | 69 |
slot under \code{useAssay} in \code{altExp(x, altExpName)}. |
70 | 70 |
Rows represent features and columns represent cells.} |
71 | 71 |
|
72 | 72 |
\item{...}{Ignored. Placeholder to prevent check warning.} |
73 | 73 |
|
74 | 74 |
\item{useAssay}{A string specifying the name of the |
75 |
-\link[SummarizedExperiment]{assay} slot to use. Default "counts".} |
|
75 |
+\link{assay} slot to use. Default "counts".} |
|
76 | 76 |
|
77 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
77 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
78 | 78 |
to use. Default "featureSubset".} |
79 | 79 |
|
80 | 80 |
\item{sampleLabel}{Vector or factor. Denotes the sample label for each cell |
... | ... |
@@ -107,12 +107,13 @@ likelihood to stop inference. Default 10.} |
107 | 107 |
\item{maxIter}{Integer. Maximum number of iterations of Gibbs sampling to |
108 | 108 |
perform. Default 200.} |
109 | 109 |
|
110 |
-\item{splitOnIter}{Integer. On every `splitOnIter` iteration, a heuristic |
|
110 |
+\item{splitOnIter}{Integer. On every \code{splitOnIter} iteration, |
|
111 |
+a heuristic |
|
111 | 112 |
will be applied to determine if a cell population or feature module should |
112 | 113 |
be reassigned and another cell population or feature module should be split |
113 | 114 |
into two clusters. To disable splitting, set to -1. Default 10.} |
114 | 115 |
|
115 |
-\item{splitOnLast}{Integer. After `stopIter` iterations have been |
|
116 |
+\item{splitOnLast}{Integer. After \code{stopIter} iterations have been |
|
116 | 117 |
performed without improvement, a heuristic will be applied to determine if |
117 | 118 |
a cell population or feature module should be reassigned and another cell |
118 | 119 |
population or feature module should be split into two clusters. If a split |
... | ... |
@@ -128,24 +129,24 @@ a default value of 12345 is used. If NULL, no calls to |
128 | 129 |
With 'random', cells are randomly assigned to a populations. With 'split', |
129 | 130 |
cells will be split into sqrt(K) populations and then each popluation will |
130 | 131 |
be subsequently split into another sqrt(K) populations. With 'predefined', |
131 |
-values in `zInit` will be used to initialize `z`. Default 'split'.} |
|
132 |
+values in \code{zInit} will be used to initialize \code{z}. Default 'split'.} |
|
132 | 133 |
|
133 | 134 |
\item{yInitialize}{Chararacter. One of 'random', 'split', or 'predefined'. |
134 | 135 |
With 'random', features are randomly assigned to a modules. With 'split', |
135 | 136 |
features will be split into sqrt(L) modules and then each module will be |
136 | 137 |
subsequently split into another sqrt(L) modules. With 'predefined', values |
137 |
-in `yInit` will be used to initialize `y`. Default 'split'.} |
|
138 |
+in \code{yInit} will be used to initialize \code{y}. Default 'split'.} |
|
138 | 139 |
|
139 |
-\item{countChecksum}{Character. An MD5 checksum for the `counts` matrix. |
|
140 |
+\item{countChecksum}{Character. An MD5 checksum for the counts matrix. |
|
140 | 141 |
Default NULL.} |
141 | 142 |
|
142 | 143 |
\item{zInit}{Integer vector. Sets initial starting values of z. If NULL, |
143 | 144 |
starting values for each cell will be randomly sampled from 1:K. 'zInit' |
144 |
-can only be used when `initialize' = 'random'`. Default NULL.} |
|
145 |
+can only be used when \code{initialize = "random"}. Default NULL.} |
|
145 | 146 |
|
146 | 147 |
\item{yInit}{Integer vector. Sets initial starting values of y. If NULL, |
147 | 148 |
starting values for each feature will be randomly sampled from 1:L. |
148 |
-'yInit' can only be used when `initialize = 'random'`. Default NULL.} |
|
149 |
+'yInit' can only be used when \code{initialize = "random"}. Default NULL.} |
|
149 | 150 |
|
150 | 151 |
\item{logfile}{Character. Messages will be redirected to a file named |
151 | 152 |
`logfile`. If NULL, messages will be printed to stdout. Default NULL.} |
... | ... |
@@ -154,21 +155,21 @@ starting values for each feature will be randomly sampled from 1:L. |
154 | 155 |
} |
155 | 156 |
\value{ |
156 | 157 |
A \linkS4class{SingleCellExperiment} object. Function |
157 |
- parameter settings are stored in \link[S4Vectors]{metadata} |
|
158 |
- \code{"celda_parameters"} in \link[SingleCellExperiment]{altExp} slot. |
|
159 |
- In \link[SingleCellExperiment]{altExp} slot, |
|
158 |
+ parameter settings are stored in \link{metadata} |
|
159 |
+ \code{"celda_parameters"} in \link{altExp} slot. |
|
160 |
+ In \link{altExp} slot, |
|
160 | 161 |
columns \code{celda_sample_label} and \code{celda_cell_cluster} in |
161 |
- \link[SummarizedExperiment]{colData} contain sample labels and celda cell |
|
162 |
+ \link{colData} contain sample labels and celda cell |
|
162 | 163 |
population clusters. Column \code{celda_feature_module} in |
163 |
- \link[SummarizedExperiment]{rowData} contains feature modules. |
|
164 |
+ \link{rowData} contains feature modules. |
|
164 | 165 |
} |
165 | 166 |
\description{ |
166 | 167 |
Clusters the rows and columns of a count matrix containing |
167 | 168 |
single-cell data into L modules and K subpopulations, respectively. The |
168 |
- \code{useAssay} \link[SummarizedExperiment]{assay} slot in |
|
169 |
- \code{altExpName} \link[SingleCellExperiment]{altExp} slot will be used if |
|
169 |
+ \code{useAssay} \link{assay} slot in |
|
170 |
+ \code{altExpName} \link{altExp} slot will be used if |
|
170 | 171 |
it exists. Otherwise, the \code{useAssay} |
171 |
- \link[SummarizedExperiment]{assay} slot in \code{x} will be used if |
|
172 |
+ \link{assay} slot in \code{x} will be used if |
|
172 | 173 |
\code{x} is a \linkS4class{SingleCellExperiment} object. |
173 | 174 |
} |
174 | 175 |
\examples{ |
... | ... |
@@ -59,9 +59,9 @@ Rows represent features and columns represent cells.} |
59 | 59 |
\item{...}{Ignored. Placeholder to prevent check warning.} |
60 | 60 |
|
61 | 61 |
\item{useAssay}{A string specifying the name of the |
62 |
-\link[SummarizedExperiment]{assay} slot to use. Default "counts".} |
|
62 |
+\link{assay} slot to use. Default "counts".} |
|
63 | 63 |
|
64 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
64 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
65 | 65 |
to use. Default "featureSubset".} |
66 | 66 |
|
67 | 67 |
\item{L}{Integer. Number of feature modules.} |
... | ... |
@@ -118,17 +118,17 @@ starting values for each feature will be randomly sampled from `1:L`. |
118 | 118 |
} |
119 | 119 |
\value{ |
120 | 120 |
A \linkS4class{SingleCellExperiment} object. Function |
121 |
- parameter settings are stored in the \link[S4Vectors]{metadata} |
|
121 |
+ parameter settings are stored in the \link{metadata} |
|
122 | 122 |
\code{"celda_parameters"} slot. Column \code{celda_feature_module} in |
123 |
- \link[SummarizedExperiment]{rowData} contains feature modules. |
|
123 |
+ \link{rowData} contains feature modules. |
|
124 | 124 |
} |
125 | 125 |
\description{ |
126 | 126 |
Clusters the rows of a count matrix containing single-cell data |
127 | 127 |
into L modules. The |
128 |
- \code{useAssay} \link[SummarizedExperiment]{assay} slot in |
|
129 |
- \code{altExpName} \link[SingleCellExperiment]{altExp} slot will be used if |
|
128 |
+ \code{useAssay} \link{assay} slot in |
|
129 |
+ \code{altExpName} \link{altExp} slot will be used if |
|
130 | 130 |
it exists. Otherwise, the \code{useAssay} |
131 |
- \link[SummarizedExperiment]{assay} slot in \code{x} will be used if |
|
131 |
+ \link{assay} slot in \code{x} will be used if |
|
132 | 132 |
\code{x} is a \linkS4class{SingleCellExperiment} object. |
133 | 133 |
} |
134 | 134 |
\examples{ |
... | ... |
@@ -49,19 +49,19 @@ using older versions of \code{celda}.} |
49 | 49 |
\item{...}{Ignored. Placeholder to prevent check warning.} |
50 | 50 |
|
51 | 51 |
\item{useAssay}{A string specifying the name of the |
52 |
-\link[SummarizedExperiment]{assay} slot to use. Default "counts".} |
|
52 |
+\link{assay} slot to use. Default "counts".} |
|
53 | 53 |
|
54 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
54 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
55 | 55 |
to use. Default "featureSubset".} |
56 | 56 |
} |
57 | 57 |
\value{ |
58 | 58 |
A \linkS4class{SingleCellExperiment} object. Function |
59 |
- parameter settings are stored in the \link[S4Vectors]{metadata} |
|
59 |
+ parameter settings are stored in the \link{metadata} |
|
60 | 60 |
\code{"celda_parameters"} slot. |
61 | 61 |
Columns \code{celda_sample_label} and \code{celda_cell_cluster} in |
62 |
- \link[SummarizedExperiment]{colData} contain sample labels and celda cell |
|
62 |
+ \link{colData} contain sample labels and celda cell |
|
63 | 63 |
population clusters. Column \code{celda_feature_module} in |
64 |
- \link[SummarizedExperiment]{rowData} contain feature modules. |
|
64 |
+ \link{rowData} contain feature modules. |
|
65 | 65 |
} |
66 | 66 |
\description{ |
67 | 67 |
Convert a old celda model object (\code{celda_C}, |
... | ... |
@@ -23,10 +23,10 @@ Rows represent features and columns represent cells.} |
23 | 23 |
|
24 | 24 |
\item{...}{Ignored. Placeholder to prevent check warning.} |
25 | 25 |
|
26 |
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} |
|
26 |
+\item{useAssay}{A string specifying which \link{assay} |
|
27 | 27 |
slot to use. Default "counts".} |
28 | 28 |
|
29 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
29 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
30 | 30 |
to use. Default "featureSubset".} |
31 | 31 |
|
32 | 32 |
\item{log}{Logical. If \code{FALSE}, then the normalized conditional |
... | ... |
@@ -39,11 +39,11 @@ labels in \code{celdaClusters(x, altExpName = altExpName)} if \code{x} is a |
39 | 39 |
|
40 | 40 |
\item{...}{Ignored. Placeholder to prevent check warning.} |
41 | 41 |
|
42 |
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} |
|
42 |
+\item{useAssay}{A string specifying which \link{assay} |
|
43 | 43 |
slot to use if \code{x} is a |
44 | 44 |
\link[SingleCellExperiment]{SingleCellExperiment} object. Default "counts".} |
45 | 45 |
|
46 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
46 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
47 | 47 |
to use. Default "featureSubset".} |
48 | 48 |
|
49 | 49 |
\item{c1}{Integer vector. Cell populations to include in group 1 for the |
... | ... |
@@ -40,11 +40,11 @@ counts matrix.} |
40 | 40 |
|
41 | 41 |
\item{...}{Ignored. Placeholder to prevent check warning.} |
42 | 42 |
|
43 |
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} |
|
43 |
+\item{useAssay}{A string specifying which \link{assay} |
|
44 | 44 |
slot to use if \code{x} is a \linkS4class{SingleCellExperiment} object. |
45 | 45 |
Default "counts".} |
46 | 46 |
|
47 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
47 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
48 | 48 |
to use. Default "featureSubset".} |
49 | 49 |
|
50 | 50 |
\item{type}{Character vector. A vector containing one or more of "counts", |
... | ... |
@@ -25,7 +25,7 @@ Rows represent features and columns represent cells.} |
25 | 25 |
\item{feature}{Character vector. Identify feature modules for the specified |
26 | 26 |
feature names. \code{feature} must match the rownames of \code{sce}.} |
27 | 27 |
|
28 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
28 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
29 | 29 |
to use. Default "featureSubset".} |
30 | 30 |
|
31 | 31 |
\item{exactMatch}{Logical. Whether to look for exactMatch of the gene name |
... | ... |
@@ -17,10 +17,10 @@ featureModuleTable( |
17 | 17 |
located in the \code{useAssay} assay slot. |
18 | 18 |
Rows represent features and columns represent cells.} |
19 | 19 |
|
20 |
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} |
|
20 |
+\item{useAssay}{A string specifying which \link{assay} |
|
21 | 21 |
slot to use. Default "counts".} |
22 | 22 |
|
23 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
23 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
24 | 24 |
to use. Default "featureSubset".} |
25 | 25 |
|
26 | 26 |
\item{outputFile}{File name for feature module table. If NULL, file will |
... | ... |
@@ -51,11 +51,11 @@ Rows represent features and columns represent cells.} |
51 | 51 |
|
52 | 52 |
\item{...}{Ignored. Placeholder to prevent check warning.} |
53 | 53 |
|
54 |
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} |
|
54 |
+\item{useAssay}{A string specifying which \link{assay} |
|
55 | 55 |
slot to use if \code{x} is a |
56 | 56 |
\link[SingleCellExperiment]{SingleCellExperiment} object. Default "counts".} |
57 | 57 |
|
58 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
58 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
59 | 59 |
to use. Default "featureSubset".} |
60 | 60 |
|
61 | 61 |
\item{class}{Vector of cell cluster labels.} |
... | ... |
@@ -27,11 +27,11 @@ matrix or \linkS4class{SingleCellExperiment} object should be gene names.} |
27 | 27 |
|
28 | 28 |
\item{...}{Ignored. Placeholder to prevent check warning.} |
29 | 29 |
|
30 |
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} |
|
30 |
+\item{useAssay}{A string specifying which \link{assay} |
|
31 | 31 |
slot to use if \code{x} is a |
32 | 32 |
\linkS4class{SingleCellExperiment} object. Default "counts".} |
33 | 33 |
|
34 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
34 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
35 | 35 |
to use. Default "featureSubset".} |
36 | 36 |
|
37 | 37 |
\item{databases}{Character vector. Name of reference database. Available |
... | ... |
@@ -29,10 +29,10 @@ Rows represent features and columns represent cells.} |
29 | 29 |
|
30 | 30 |
\item{...}{Ignored. Placeholder to prevent check warning.} |
31 | 31 |
|
32 |
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} |
|
32 |
+\item{useAssay}{A string specifying which \link{assay} |
|
33 | 33 |
slot to use. Default "counts".} |
34 | 34 |
|
35 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
35 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
36 | 36 |
to use. Default "featureSubset".} |
37 | 37 |
} |
38 | 38 |
\value{ |
... | ... |
@@ -19,7 +19,7 @@ model object.} |
19 | 19 |
|
20 | 20 |
\item{...}{Ignored. Placeholder to prevent check warning.} |
21 | 21 |
|
22 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
22 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
23 | 23 |
to use. Default "featureSubset".} |
24 | 24 |
} |
25 | 25 |
\value{ |
... | ... |
@@ -46,11 +46,11 @@ Rows represent features and columns represent cells.} |
46 | 46 |
|
47 | 47 |
\item{...}{Additional parameters passed to \link[ComplexHeatmap]{Heatmap}.} |
48 | 48 |
|
49 |
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} |
|
49 |
+\item{useAssay}{A string specifying which \link{assay} |
|
50 | 50 |
slot to use if \code{x} is a |
51 | 51 |
\linkS4class{SingleCellExperiment} object. Default "counts".} |
52 | 52 |
|
53 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
53 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
54 | 54 |
to use. Default "featureSubset".} |
55 | 55 |
|
56 | 56 |
\item{featureModule}{Integer Vector. The featureModule(s) to display. |
... | ... |
@@ -39,11 +39,11 @@ counts matrix.} |
39 | 39 |
|
40 | 40 |
\item{...}{Ignored. Placeholder to prevent check warning.} |
41 | 41 |
|
42 |
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} |
|
42 |
+\item{useAssay}{A string specifying which \link{assay} |
|
43 | 43 |
slot to use if \code{x} is a \linkS4class{SingleCellExperiment} object. |
44 | 44 |
Default "counts".} |
45 | 45 |
|
46 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
46 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
47 | 47 |
to use. Default "featureSubset".} |
48 | 48 |
|
49 | 49 |
\item{newCounts}{A new counts matrix used to calculate perplexity. If NULL, |
... | ... |
@@ -36,11 +36,11 @@ represent features and columns represent cells.} |
36 | 36 |
|
37 | 37 |
\item{features}{Character vector. Uses these genes for plotting.} |
38 | 38 |
|
39 |
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} |
|
39 |
+\item{useAssay}{A string specifying which \link{assay} |
|
40 | 40 |
slot to use if \code{x} is a |
41 | 41 |
\linkS4class{SingleCellExperiment} object. Default "counts".} |
42 | 42 |
|
43 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
43 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
44 | 44 |
to use. Default "featureSubset".} |
45 | 45 |
|
46 | 46 |
\item{exactMatch}{Logical. Whether an exact match or a partial match using |
... | ... |
@@ -49,7 +49,7 @@ column in \code{colData(x)}.} |
49 | 49 |
\linkS4class{SingleCellExperiment} object. Ignored if both \code{dim1} and |
50 | 50 |
\code{dim2} are set.} |
51 | 51 |
|
52 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
52 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
53 | 53 |
to use. Default "featureSubset".} |
54 | 54 |
|
55 | 55 |
\item{dim1}{Numeric vector. First dimension from data |
... | ... |
@@ -73,11 +73,11 @@ dimension reduction output.} |
73 | 73 |
\item{dim2}{Numeric vector. Second dimension from data dimension |
74 | 74 |
reduction output.} |
75 | 75 |
|
76 |
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} |
|
76 |
+\item{useAssay}{A string specifying which \link{assay} |
|
77 | 77 |
slot to use if \code{x} is a |
78 | 78 |
\linkS4class{SingleCellExperiment} object. Default "counts".} |
79 | 79 |
|
80 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
80 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
81 | 81 |
to use. Default "featureSubset".} |
82 | 82 |
|
83 | 83 |
\item{features}{Character vector. Features in the rownames of counts to plot.} |
... | ... |
@@ -99,7 +99,7 @@ and standard deviation of 1. Default \code{TRUE}.} |
99 | 99 |
and upper bounds for the data. This threshold is applied after row scaling. |
100 | 100 |
Set to NULL to disable. Default \code{c(-1,1)}.} |
101 | 101 |
|
102 |
-\item{limits}{Passed to \link[ggplot2]{scale_colour_gradient2}. The range |
|
102 |
+\item{limits}{Passed to \link{scale_colour_gradient2}. The range |
|
103 | 103 |
of color scale.} |
104 | 104 |
|
105 | 105 |
\item{size}{Numeric. Sets size of point on plot. Default 1.} |
... | ... |
@@ -65,11 +65,11 @@ reduction output.} |
65 | 65 |
\item{dim2}{Numeric vector. Second dimension from data dimension |
66 | 66 |
reduction output.} |
67 | 67 |
|
68 |
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} |
|
68 |
+\item{useAssay}{A string specifying which \link{assay} |
|
69 | 69 |
slot to use if \code{x} is a |
70 | 70 |
\linkS4class{SingleCellExperiment} object. Default "counts".} |
71 | 71 |
|
72 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
72 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
73 | 73 |
to use. Default "featureSubset".} |
74 | 74 |
|
75 | 75 |
\item{size}{Numeric. Sets size of point on plot. Default 1.} |
... | ... |
@@ -78,7 +78,7 @@ to use. Default "featureSubset".} |
78 | 78 |
|
79 | 79 |
\item{ylab}{Character vector. Label for the y-axis. Default 'Dimension_2'.} |
80 | 80 |
|
81 |
-\item{limits}{Passed to \link[ggplot2]{scale_colour_gradient2}. The range |
|
81 |
+\item{limits}{Passed to \link{scale_colour_gradient2}. The range |
|
82 | 82 |
of color scale.} |
83 | 83 |
|
84 | 84 |
\item{colorLow}{Character. A color available from `colors()`. |
... | ... |
@@ -63,11 +63,11 @@ First dimension from data dimension reduction output.} |
63 | 63 |
\item{dim2}{Numeric vector. |
64 | 64 |
Second dimension from data dimension reduction output.} |
65 | 65 |
|
66 |
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} |
|
66 |
+\item{useAssay}{A string specifying which \link{assay} |
|
67 | 67 |
slot to use if \code{x} is a |
68 | 68 |
\linkS4class{SingleCellExperiment} object. Default "counts".} |
69 | 69 |
|
70 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
70 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
71 | 71 |
to use. Default "featureSubset".} |
72 | 72 |
|
73 | 73 |
\item{modules}{Character vector. Module(s) from celda model to be plotted. |
... | ... |
@@ -76,7 +76,7 @@ e.g. c("1", "2").} |
76 | 76 |
\item{rescale}{Logical. |
77 | 77 |
Whether rows of the matrix should be rescaled to [0, 1]. Default TRUE.} |
78 | 78 |
|
79 |
-\item{limits}{Passed to \link[ggplot2]{scale_colour_gradient}. The range |
|
79 |
+\item{limits}{Passed to \link{scale_colour_gradient}. The range |
|
80 | 80 |
of color scale.} |
81 | 81 |
|
82 | 82 |
\item{size}{Numeric. Sets size of point on plot. Default 1.} |
... | ... |
@@ -23,7 +23,7 @@ plotGridSearchPerplexity(x, ...) |
23 | 23 |
|
24 | 24 |
\item{...}{Ignored. Placeholder to prevent check warning.} |
25 | 25 |
|
26 |
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot |
|
26 |
+\item{altExpName}{The name for the \link{altExp} slot |
|
27 | 27 |
to use. Default "featureSubset".} |
28 | 28 |
|
29 | 29 |
\item{sep}{Numeric. Breaks in the x axis of the resulting plot.} |