Dear developers,
I have just downloaded SpatialOmicsOverlay and I am hoping to plot some gene expression data from a GeoMx object to an OME-TIFF file that I downloaded from the GeoMx DSP Control Center (which I think is hosted by my university). I am following the steps noted in this vignette.
I have downloaded the OME-TIFF file and I am now trying to run readSpatialOverlay, but I get an error:
Error in if (nrow(AOIattrs) < nrow(annots)) { :
argument is of length zero
2. parseOverlayAttrs(omexml = xml, annots = annots, labworksheet = labWorksheet)
1. readSpatialOverlay(ometiff = "../GeoMx Images/GeoMx OME-TIFF Files/220520-18PL-20291 01-02-Scan 2.ome.tiff",
annots = "../GeoMx Data/GeoMx Raw Data/p2112_20220916T1419_LabWorksheetExpanded.csv",
slideName = "18PL-20291 01-02", image = FALSE, saveFile = FALSE, outline = FALSE)
Would somebody be able to help me understand what nrow(AOIattrs) refers to?
The OME-TIFF file that I downloaded should have around 19 regions of interest selected; the annotations file that I am using has annotations for 125 regions of interest (for this slide and a few others). There are also two rows for No Template Control. I have, however, tried to use an Excel worksheet with only the 19 regions of interest from this slide.
For reference, these are the column names in the worksheet that I am using (p2112_20220916T1419_LabWorksheetExpanded.csv, the worksheet with annotations for all 125 regions of interest), and the first five rows. As you can see, there is both information regarding the scan, but also some metadata which I would like to carry with me. Should any column names be changed so that the above function will work?
Dear developers, I have just downloaded
SpatialOmicsOverlayand I am hoping to plot some gene expression data from a GeoMx object to an OME-TIFF file that I downloaded from the GeoMx DSP Control Center (which I think is hosted by my university). I am following the steps noted in this vignette. I have downloaded the OME-TIFF file and I am now trying to runreadSpatialOverlay, but I get an error:This is the error message that I receive:
Would somebody be able to help me understand what
nrow(AOIattrs)refers to? The OME-TIFF file that I downloaded should have around 19 regions of interest selected; the annotations file that I am using has annotations for 125 regions of interest (for this slide and a few others). There are also two rows forNo Template Control. I have, however, tried to use an Excel worksheet with only the 19 regions of interest from this slide. For reference, these are the column names in the worksheet that I am using (p2112_20220916T1419_LabWorksheetExpanded.csv, the worksheet with annotations for all 125 regions of interest), and the first five rows. As you can see, there is both information regarding the scan, but also some metadata which I would like to carry with me. Should any column names be changed so that the above function will work?<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">
| Sample_ID | slide name | scan name | panel | ROILabel | segment | aoi | area | tags | ROI_ID_1 | SlideName | ScanLabel | RawReads | AlignedReads | DeduplicatedReads | StitchedReads | TrimmedReads | AOINucleiCount | AOISurfaceArea | ScanHeight | ScanWidth | Scan_Date | ROICoordinateX | ROICoordinateY | NormalizationFactor | QCFlags | Patient | Patient_GeoMx | Tissue | Type | Type_English -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- 1 | DSP-1001660006454-G-A01 | No Template Control | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA 2 | DSP-1001660006454-G-A02 | 19PL-12941 01-02 | 220519-19PL-12941 01-02-Scan 1 | (v1.0) Human NGS Whole Transcriptome Atlas RNA | 001_I | Full ROI | Full ROI-aoi-001 | 32672.83 | NA | 001_I | 19PL-12941 01-02 | 220519-19PL-12941 01-02-Scan 1 | 5314100 | 4645056 | 923823 | 4738679 | 4748882 | 293 | 32672.83 | 51945.28 | 26117.81 | 220519 | 13860 | 30805 | 0.863753 | NA | 24 | 41 | I | I | I 3 | DSP-1001660006454-G-A03 | 19PL-12941 01-02 | 220519-19PL-12941 01-02-Scan 1 | (v1.0) Human NGS Whole Transcriptome Atlas RNA | 002_I | Full ROI | Full ROI-aoi-001 | 37725.01 | NA | 002_I | 19PL-12941 01-02 | 220519-19PL-12941 01-02-Scan 1 | 5025289 | 4377359 | 766415 | 4467791 | 4476590 | 295 | 37725.01 | 51945.28 | 26117.81 | 220519 | 14226 | 30353 | 1.046973 | NA | 24 | 41 | I | I | I 4 | DSP-1001660006454-G-A04 | 19PL-12941 01-02 | 220519-19PL-12941 01-02-Scan 1 | (v1.0) Human NGS Whole Transcriptome Atlas RNA | 003_TI | Full ROI | Full ROI-aoi-001 | 41630.05 | NA | 003_TI | 19PL-12941 01-02 | 220519-19PL-12941 01-02-Scan 1 | 5681850 | 4796496 | 878048 | 4905337 | 4915221 | 218 | 41630.05 | 51945.28 | 26117.81 | 220519 | 13014 | 31401 | 0.50809 | NA | 24 | 41 | T | TI | TE 5 | DSP-1001660006454-G-A05 | 19PL-12941 01-02 | 220519-19PL-12941 01-02-Scan 1 | (v1.0) Human NGS Whole Transcriptome Atlas RNA | 004_TI | Full ROI | Full ROI-aoi-001 | 35196.62 | NA | 004_TI | 19PL-12941 01-02 | 220519-19PL-12941 01-02-Scan 1 | 3691514 | 3121196 | 636215 | 3192486 | 3199437 | 162 | 35196.62 | 51945.28 | 26117.81 | 220519 | 13003 | 32921 | 0.677453 | NA | 24 | 41 | T | TI | TE