| ... | ... |
@@ -95,8 +95,63 @@ importMultipleSources <- function(allImportEntries, delayedArray = FALSE) {
|
| 95 | 95 |
} |
| 96 | 96 |
|
| 97 | 97 |
} |
| 98 |
+ |
|
| 99 |
+ # Begin Set Tags |
|
| 100 |
+ if(entry$type %in% c("cellRanger2", "cellRanger3", "starSolo", "busTools", "seqc", "optimus", "example")){
|
|
| 101 |
+ newSce <- expSetDataTag( |
|
| 102 |
+ inSCE = newSce, |
|
| 103 |
+ assayType = "raw", |
|
| 104 |
+ assays = assayNames(newSce)) |
|
| 105 |
+ } |
|
| 106 |
+ else if(entry$type %in% c("rds", "files")){
|
|
| 107 |
+ # Check if tags already stored in uploaded rds/files |
|
| 108 |
+ if(is.null(metadata(newSce)$assayType)){
|
|
| 109 |
+ try({
|
|
| 110 |
+ counts(newSce) |
|
| 111 |
+ newSce <- expSetDataTag( |
|
| 112 |
+ inSCE = newSce, |
|
| 113 |
+ assayType = "raw", |
|
| 114 |
+ assays = "counts") |
|
| 115 |
+ }, silent = TRUE) |
|
| 116 |
+ |
|
| 117 |
+ try({
|
|
| 118 |
+ logcounts(newSce) |
|
| 119 |
+ newSce <- expSetDataTag( |
|
| 120 |
+ inSCE = newSce, |
|
| 121 |
+ assayType = "transformed", |
|
| 122 |
+ assays = "logcounts") |
|
| 123 |
+ }, silent = TRUE) |
|
| 124 |
+ |
|
| 125 |
+ try({
|
|
| 126 |
+ normcounts(newSce) |
|
| 127 |
+ newSce <- expSetDataTag( |
|
| 128 |
+ inSCE = newSce, |
|
| 129 |
+ assayType = "transformed", |
|
| 130 |
+ assays = "normcounts") |
|
| 131 |
+ }, silent = TRUE) |
|
| 132 |
+ |
|
| 133 |
+ try({
|
|
| 134 |
+ decontXcounts(newSce) |
|
| 135 |
+ newSce <- expSetDataTag( |
|
| 136 |
+ inSCE = newSce, |
|
| 137 |
+ assayType = "raw", |
|
| 138 |
+ assays = "decontXcounts") |
|
| 139 |
+ }, silent = TRUE) |
|
| 140 |
+ |
|
| 141 |
+ untaggedAssays <- assayNames(newSce) |
|
| 142 |
+ untaggedAssays <- untaggedAssays[! untaggedAssays %in% c('counts', 'logcounts', 'normcounts', 'decontX')]
|
|
| 143 |
+ |
|
| 144 |
+ newSce <- expSetDataTag( |
|
| 145 |
+ inSCE = newSce, |
|
| 146 |
+ assayType = "uncategorized", |
|
| 147 |
+ assays = untaggedAssays) |
|
| 148 |
+ } |
|
| 149 |
+ # End Set Tags |
|
| 150 |
+ } |
|
| 151 |
+ |
|
| 98 | 152 |
sceObjs = c(sceObjs, list(newSce)) |
| 99 | 153 |
} |
| 154 |
+ |
|
| 100 | 155 |
return(combineSCE(sceList = sceObjs, |
| 101 | 156 |
by.r = Reduce(base::intersect, lapply(sceObjs, function(x) { colnames(rowData(x))})),
|
| 102 | 157 |
by.c = Reduce(base::intersect, lapply(sceObjs, function(x) { colnames(colData(x))})),
|
| ... | ... |
@@ -27,11 +27,10 @@ expDeleteDataTag <- function(inSCE, assay){
|
| 27 | 27 |
#' @param inSCE Input \code{SingleCellExperiment} object.
|
| 28 | 28 |
#' @param assayType Specify a \code{character(1)} value as a tag that should be set against a data item.
|
| 29 | 29 |
#' @param assays Specify name(s) \code{character()} of data item(s) against which the tag should be set.
|
| 30 |
-#' @param append A \code{logical} value indicating if this assay should be appended to the object or overridden. Default value is \code{TRUE} indicating that it should be appended.
|
|
| 31 | 30 |
#' @return The input \code{SingleCellExperiment} object with tag information stored in the metadata slot.
|
| 32 | 31 |
#' @export |
| 33 | 32 |
#' |
| 34 |
-expSetDataTag <- function(inSCE, assayType, assays, append = TRUE){
|
|
| 33 |
+expSetDataTag <- function(inSCE, assayType, assays){
|
|
| 35 | 34 |
tbl <- NULL |
| 36 | 35 |
if(is.null(S4Vectors::metadata(inSCE)$assayType)){
|
| 37 | 36 |
tbl <- tibble::tibble(assayTag = assayType, assayName = assays) |
| ... | ... |
@@ -865,13 +865,12 @@ shinyServer(function(input, output, session) {
|
| 865 | 865 |
if (!is.null(vals$original)) {
|
| 866 | 866 |
vals$counts <- vals$original |
| 867 | 867 |
#store assayType information in the metadata |
| 868 |
- if (!"assayType" %in% names(metadata(vals$counts))) {
|
|
| 869 |
- vals$counts <- expSetDataTag( |
|
| 870 |
- inSCE = vals$counts, |
|
| 871 |
- assayType = "raw", |
|
| 872 |
- assays = assayNames(vals$counts), |
|
| 873 |
- append = FALSE) |
|
| 874 |
- } |
|
| 868 |
+ # if (!"assayType" %in% names(metadata(vals$counts))) {
|
|
| 869 |
+ # vals$counts <- expSetDataTag( |
|
| 870 |
+ # inSCE = vals$counts, |
|
| 871 |
+ # assayType = "raw", |
|
| 872 |
+ # assays = assayNames(vals$counts)) |
|
| 873 |
+ # } |
|
| 875 | 874 |
if (any(duplicated(rownames(vals$counts)))) {
|
| 876 | 875 |
warning("Duplicated rownames detected, making them unique...")
|
| 877 | 876 |
vals$counts <- dedupRowNames(vals$counts) |
| ... | ... |
@@ -5,7 +5,7 @@ |
| 5 | 5 |
\title{expSetDataTag
|
| 6 | 6 |
Set tag to an assay or a data item in the input SCE object.} |
| 7 | 7 |
\usage{
|
| 8 |
-expSetDataTag(inSCE, assayType, assays, append = TRUE) |
|
| 8 |
+expSetDataTag(inSCE, assayType, assays) |
|
| 9 | 9 |
} |
| 10 | 10 |
\arguments{
|
| 11 | 11 |
\item{inSCE}{Input \code{SingleCellExperiment} object.}
|
| ... | ... |
@@ -13,8 +13,6 @@ expSetDataTag(inSCE, assayType, assays, append = TRUE) |
| 13 | 13 |
\item{assayType}{Specify a \code{character(1)} value as a tag that should be set against a data item.}
|
| 14 | 14 |
|
| 15 | 15 |
\item{assays}{Specify name(s) \code{character()} of data item(s) against which the tag should be set.}
|
| 16 |
- |
|
| 17 |
-\item{append}{A \code{logical} value indicating if this assay should be appended to the object or overridden. Default value is \code{TRUE} indicating that it should be appended.}
|
|
| 18 | 16 |
} |
| 19 | 17 |
\value{
|
| 20 | 18 |
The input \code{SingleCellExperiment} object with tag information stored in the metadata slot.
|
