akoyabio / phenoptrReports

Create analysis reports from inForm data.
https://akoyabio.github.io/phenoptrReports
zlib License
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Using Phenoptr reports with non-Vectra TIFFs #42

Closed man154 closed 3 years ago

man154 commented 3 years ago

I have a multi-layered TIFF which I generated from a multi-channel fluorescence image. I also have the corresponding RGB/flattened/composite image. I wish to make a spatial distance map with phenoptrReports. The Spatial Map Viewer can locate the file, but throws this error. Any suggestion?

Warning in min(x) : no non-missing arguments to min; returning Inf Warning in max(x) : no non-missing arguments to max; returning -Inf Warning in min(x) : no non-missing arguments to min; returning Inf Warning in max(x) : no non-missing arguments to max; returning -Inf Warning: Removed 1 rows containing missing values (geom_segment). Warning: Removed 1 rows containing missing values (geom_text). Warning in min(x) : no non-missing arguments to min; returning Inf Warning in max(x) : no non-missing arguments to max; returning -Inf Warning in min(x) : no non-missing arguments to min; returning Inf Warning in max(x) : no non-missing arguments to max; returning -Inf Warning: Removed 1 rows containing missing values (geom_segment). Warning: Removed 1 rows containing missing values (geom_text). Warning in min(x) : no non-missing arguments to min; returning Inf Warning in max(x) : no non-missing arguments to max; returning -Inf Warning in min(x) : no non-missing arguments to min; returning Inf Warning in max(x) : no non-missing arguments to max; returning -Inf Warning: Error in grid.Call.graphics: non-finite location and/or size for viewport 178: recordGraphics 177: grid.draw.gTree 175: print.ggplot 167: func 165: f 164: Reduce 155: do 154: hybrid_chain 126: drawPlot 112: 96: drawReactive 83: renderFunc 82: output$plot 2: shiny::runApp 1: phenoptrReports::spatial_map_viewer

AB-Kent commented 3 years ago

The spatial map viewer relies on spatial reference information in the component data files written by inForm. Your TIFF file probably does not include this.