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akoyabio / phenoptrReports

Create analysis reports from inForm data.
https://akoyabio.github.io/phenoptrReports
zlib License
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Data Consolidation creates duplicate columns instead of merging #45

Closed cduerrschmid closed 3 years ago

cduerrschmid commented 3 years ago

I am consolidating merged cell seg data from 3 binary phenotyping projects. the output consolidated_data.txt has a ".x" or ".y" added to the end of each column. There are "duplicate" columns, like Sample Name.x/Sample Name.y etc. This project worked just fine with a prior version of PR (of course I don't know which one, since that information is gone after updating everything). The consolidated_data.html still seems fine, however the txt can't be used for spatial analysis. Consolidated_data.txt Consolidated_data.zip merge cell seg data.zip

Console output is pretty much useless, as there is no error returned : "R version 4.1.0 (2021-05-18) -- "Camp Pontanezen" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.

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Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.

phenoptrReports:::addin_10_merge() Loading required package: shiny

Listening on http://127.0.0.1:4412

phenoptrReports:::addin_10_merge()

Listening on http://127.0.0.1:4412

phenoptrReports:::addin_10_merge()

Listening on http://127.0.0.1:4412

phenoptrReports:::addin_20_consolidate()

Listening on http://127.0.0.1:4412 Reading "CD3_Merge_cell_seg_data". Data is already in microns, no conversion performed
Writing report for "CD3_Merge_cell_seg_data". Loading required package: UpSetR Reading "FoxP3_Merge_cell_seg_data". Data is already in microns, no conversion performed
Writing report for "FoxP3_Merge_cell_seg_data". Reading "Ki67_Merge_cell_seg_data". Data is already in microns, no conversion performed
Writing report for "Ki67_Merge_cell_seg_data". Writing consolidated data. Writing report for consolidated data.
Done!

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AB-Kent commented 3 years ago

Fixed now, thanks for the report!