H-Score report fix #63
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HIMSR noticed an issue with the H-Score report in phenoptrReports being noticeably off. Akoya offered a possible explanation: Cells without valid compartment measurements (missing cytoplasm with corresponding mean intensities given as `#N/A`) are erroneously put into the 3+ category. This fix places all intensity measurements with numerical values (existing cell compartment) into their respective H-Score categories, while ignoring all non-numerical (`#N/A`) values. Notice that this means that cells without valid compartments are not reported in the H-score summary.
Error message was: ```> write_h_score_sheet(wb, h_score_1) Warning: Error in str_replace_all: `string` must be a vector, not a symbol. 2: shiny::runApp 1: phenoptrReports:::addin_30_analysis_app ``` It turns out that the function `remove_marker_mean` is called with a symbol instead of a string. The fix avoids side effects by casting the function argument `s` to string before use.
`sum(1:3, NA)` evaluates to `NA`, if the `na.rm` parameter is not set to remove `NA` values prior to calculating the sum.
``` Returning data frames from `filter()` expressions was deprecated in dplyr 1.0.8. ℹ Please use `if_any()` or `if_all()` instead. ℹ The deprecated feature was likely used in the phenoptrReports package. Please report the issue at <https://github.com/akoyabio/phenoptrReports/issues>. ```
``` ── Warning (test_smoke.R:136:3): file generation works ───────────────────────── `cross2()` was deprecated in purrr 1.0.0. i Please use `tidyr::expand_grid()` instead. i See <tidyverse/purrr#768>. ```
When comparing H-Score values from (previous) `phenoptrReports` and (current) `inForm`, it's important to understand that both scored missing measurements into extreme categories (`3+`/`0+`) skewing the reported values depending on the number of missing measurements. The current version of `phenoptrReports` omits missing measurements completely and reports adjusted counts and percentages.
When a specific phenotype hasn't been identified for a particular slide, the H-Scores were erroneously reported as `FALSE` values. This fix inserts missing counts as `NA` values.
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Aim of this PR is to address an issue with
phenoptrReportwhen reporting H-Score values for cells missing mean pixel intensity measurements (#N/A). Measurement can be missing when the corresponding cellular compartment (cytoplasm, membrane) is missing as a result of cell segmentation. Cells mostly affected will be those located in densely packed clusters, where the cell expansion of the cytoplasm failed due to the presence of neighboring cells in close proximity.3+categoryIt has to be noted that the results of the fixed version of
phenoptrReportsmay deviate frominForm.0+categoryAs part of QC, compare the total number of cells reported in the
Cell Countstab with the corresponding total number of cells in the individualH-Scoretabs. A significant reduction of available cells for the H-Score calculation indicates cell segmentation issues. As a workaround, a different, physiologically relevant, compartment may be selected for scoring.phenoptrReportspasses all tests without warnings.