Hello, My name is Shweta Johari and I have multiple IHC projects and want to analyze them using phnoptr R. I have downloaded the phenoptr according to the installation instructions in the pdf link below: https://d1fgrgbaaj3jvk.cloudfront.net/wp-content/uploads/2020/05/PhenoptrRerports_Install_Instructions.v5.pdf

However, I merged my data using inFORM but when I use the consolidated and summary in R addins. I only receive one summary report HTML of one project and not two. The two projects do not get consolidated or summarised.

I am receiving the following: phenoptrReports:::addin_20_consolidate() Loading required package: shiny

Listening on http://127.0.0.1:7199 Reading "merged_f4-80_sma_cd31_cell_seg_data". Data is already in microns, no conversion performed
Adding Slide ID column to merged_f4-80_sma_cd31_cell_seg_data.txt Writing report for "merged_f4-80_sma_cd31_cell_seg_data". Loading required package: UpSetR Quitting from lines 174-196 (Cell_seg_summary_report.Rmd) Unable to write summary report All renaming inputs must be named. Reading "mhc2 vim_cell_seg_data". Data is already in microns, no conversion performed
Adding Slide ID column to mhc2 vim_cell_seg_data.txt Writing report for "mhc2 vim_cell_seg_data". geom_path: Each group consists of only one observation. Do you need to adjust the group aesthetic? geom_path: Each group consists of only one observation. Do you need to adjust the group aesthetic? Writing consolidated data. Writing report for consolidated data.
Quitting from lines 174-196 (Cell_seg_summary_report.Rmd) Unable to write summary report All renaming inputs must be named. Done! >

Does anyone know what is going wrong please? I am using the latest R version as well as phnoptr. Can someone please help me?

Thanking you. Shweta Johari