Adds markers to the data

The function adds a 'markers' feature variable. These markers are read from a comma separated values (csv) spreadsheet file. This markers file is expected to have 2 columns (others are ignored) where the first is the name of the marker features and the second the group label. Alternatively, a markers named vector as provided by the pRolocmarkers function can also be used.

addMarkers(object, markers, mcol = "markers", fcol, verbose = TRUE)

Arguments

object

An instance of class MSnSet.

markers

A character with the name the markers' csv file or a named character of markers as provided by pRolocmarkers.

mcol

A character of length 1 defining the feature variable label for the newly added markers. Default is "markers".

fcol

An optional feature variable to be used to match against the markers. If missing, the feature names are used.

verbose

A logical indicating if number of markers and marker table should be printed to the console.

Value

A new instance of class MSnSet with an additional markers feature variable.

Details

It is essential to assure that featureNames(object) (or fcol, see below) and marker names (first column) match, i.e. the same feature identifiers and case fold are used.

See also

See pRolocmarkers for a list of spatial markers and markers for details about markers encoding.

Author

Laurent Gatto

Examples

library("pRolocdata")
data(dunkley2006)
atha <- pRolocmarkers("atha")
try(addMarkers(dunkley2006, atha)) ## markers already exists
#> Error in addMarkers(dunkley2006, atha) : 
#>   Detected an existing 'markers' feature column.
fData(dunkley2006)$markers.org <- fData(dunkley2006)$markers
fData(dunkley2006)$markers <- NULL
marked <- addMarkers(dunkley2006, atha)
#> Markers in data: 255 out of 689
#> organelleMarkers
#>           ENV            ER      ER lumen   ER membrane         Golgi 
#>             3            21             9            42            27 
#> Mitochondrion            PM       Plastid      Ribosome           STR 
#>            50            42            22             8             2 
#>           TGN       Vacuole       unknown 
#>            13            16           434 
fvarLabels(marked)
#> [1] "assigned"     "evidence"     "method"       "new"          "pd.2013"     
#> [6] "pd.markers"   "markers.orig" "markers.org"  "markers"     
## if 'makers' already exists
marked <- addMarkers(marked, atha, mcol = "markers2")
#> Markers in data: 255 out of 689
#> organelleMarkers
#>           ENV            ER      ER lumen   ER membrane         Golgi 
#>             3            21             9            42            27 
#> Mitochondrion            PM       Plastid      Ribosome           STR 
#>            50            42            22             8             2 
#>           TGN       Vacuole       unknown 
#>            13            16           434 
fvarLabels(marked)
#>  [1] "assigned"     "evidence"     "method"       "new"          "pd.2013"     
#>  [6] "pd.markers"   "markers.orig" "markers.org"  "markers"      "markers2"    
stopifnot(all.equal(fData(marked)$markers, fData(marked)$markers2))
plot2D(marked)
addLegend(marked, where = "topleft", cex = .7)