FAQ

My SpatialExperiment contains ENSEMBL IDs. Can i still perform deconvolution?

It is possible to perform second-generation deconvolution algorithms when annotated scRNA-seq data containing ENSEMBL IDs is available. All first-gen deconvolution tools require HGNC symbols. You may also check your SpatialExperiment rowData() for available annotation to overwrite ENSEMBL IDs. In most cases this can be solved by using the following code:

rownames(spe) <- rowData(spe)$symbol

How can i see which deconvolution results are available in my object?

You can use available_results(object) or access names(colData(object)) to see which deconvolution results are available.

The spacedeconv plots contain a lot of white spots

When reading raw spatial data the SpatialExperiment contains expression information for all spots, even if they are not located over tissue. Remove those spots with the following code

spe <- spe[, colData(spe)$in_tissue == TRUE]

The Visium Slide and the spatial data are not rotated in the same direction

The SpatialExperiment wrapper includes function to rotate/mirror the image. More information can be found in the Visualization Vignette or the SpatialExperiment Documentation.

The hexagons in my plots are rotated and don’t give an even appearance

Your Visium slide might be aligned incorrectly. Try rotating the image or use offset_rotation=TRUE as a parameter in the plotting function.

Which deconvolution tools are available?

This list includes the methods name and the internally used tokens. More detailed descriptions of each method can be found at the end of this vignette.

spacedeconv::deconvolution_methods

## The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
## which was just loaded, will retire in October 2023.
## Please refer to R-spatial evolution reports for details, especially
## https://r-spatial.org/r/2023/05/15/evolution4.html.
## It may be desirable to make the sf package available;
## package maintainers should consider adding sf to Suggests:.
## The sp package is now running under evolution status 2
##      (status 2 uses the sf package in place of rgdal)

## Configuring package 'spacedeconv': please wait ...

## Done!

##             RCTD        SPOTlight             CARD      spatialDWLS 
##           "rctd"      "spotlight"           "card"    "spatialdwls" 
##    cell2location        AutoGeneS       BayesPrism           Bisque 
##  "cell2location"      "autogenes"     "bayesprism"         "bisque" 
##          BSeq-sc       CIBERSORTx            CDSeq              CPM 
##         "bseqsc"     "cibersortx"          "cdseq"            "cpm" 
##             DWLS             MOMF            MuSiC           Scaden 
##           "dwls"           "momf"          "music"         "scaden" 
##             SCDC       MCPcounter             EPIC        quanTIseq 
##           "scdc"    "mcp_counter"           "epic"      "quantiseq" 
##            xCell        CIBERSORT CIBERSORT (abs.)            TIMER 
##          "xcell"      "cibersort"  "cibersort_abs"          "timer" 
##     ConsensusTME             ABIS         ESTIMATE      mMCPcounter 
##  "consensus_tme"           "abis"       "estimate"   "mmcp_counter" 
##        seqImmuCC              DCQ             BASE 
##      "seqimmucc"            "dcq"           "base"

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