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akoyabio / phenoptr

Helper functions for working with inForm data.
https://akoyabio.github.io/phenoptr/
zlib License
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phnoptr is updated but yet positive phenotype error is being showed. #20

Open db7007 opened 2 years ago

db7007 commented 2 years ago

Respected Sir, Greetings of the season. I have the following error after merging the data and then I tried to consolidate it.

remotes::install_github('akoyabio/phenoptr@9000') Skipping install of 'phenoptr' from a github remote, the SHA1 (7d5dceaa) has not changed since last install. Use force = TRUE to force installation remotes::install_github('akoyabio/phenoptrReports@9000') Skipping install of 'phenoptrReports' from a github remote, the SHA1 (af94a14c) has not changed since last install. Use force = TRUE to force installation

phenoptrReports:::addin_20_consolidate()

Listening on http://127.0.0.1:4908 Reading "CD4+ PHENOTYPING ALL_Merge_cell_seg_data". Data is already in microns, no conversion performed
Adding Slide ID column to Merge_cell_seg_data.txt Writing report for "CD4+ PHENOTYPING ALL_Merge_cell_seg_data". Loading required package: UpSetR Reading "CD8+ PHENOTYPING ALL_Merge_cell_seg_data". Data is already in microns, no conversion performed
Adding Slide ID column to Merge_cell_seg_data.txt Writing report for "CD8+ PHENOTYPING ALL_Merge_cell_seg_data". Reading "foxp3+lymphoid_Merge_cell_seg_data". Data is already in microns, no conversion performed
Adding Slide ID column to Merge_cell_seg_data.txt Writing report for "foxp3+lymphoid_Merge_cell_seg_data". Reading "NKP46+PHENOTYPING ALL_Merge_cell_seg_data". Data is already in microns, no conversion performed
Adding Slide ID column to Merge_cell_seg_data.txt Warning: Error in split_phenotype_column: No positive phenotypes found in column "Phenotype". 3: shiny::runApp 2: shiny::runGadget 1: phenoptrReports:::addin_20_consolidate

Ran on: RStudio 2021.09.1+372 "Ghost Orchid" Release (8b9ced188245155642d024aa3630363df611088a, 2021-11-08) for macOS Mozilla/5.0 (Macintosh; Intel Mac OS X 12_0_1) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36

AB-Kent commented 2 years ago

What are the values in the Phenotype column of "NKP46+PHENOTYPING ALL_Merge_cell_seg_data" ? Does it contain any values ending in "+" ?

shwetajohari commented 2 years ago

Good afternoon Sir, Facing a similar issue, there are no values that end with + in the column. How do I change that please? Do I have to re-phenotype on inform?

Looking forward to your response.

Yours sincerely, Shweta Johari

AB-Kent commented 2 years ago

Yes, to use phenoptr, your positive phenotypes must have names ending in +. You can re-name them in inForm or edit the inForm output files change this.

shwetajohari commented 2 years ago

Respected Sir, I have added the “+” sign as well as there is no space or hypen between the name and sign. In my other project also I can only see one positive Cd8+ but in the images there are so many. How do I go ahead with This? Looking forward to your reply. Yours sincerely, Shweta Johari

On Tuesday, January 18, 2022, Kent Johnson @.***> wrote:

Yes, to use phenoptr, your positive phenotypes must have names ending in +. You can re-name them in inForm or edit the inForm output files change this.

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AB-Kent commented 2 years ago

Please ask your local FAS for help.