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* bug: standard curve sample type (#13) * simple README with overview and installation (#7) * website for docs (#8) * add sample vignette and artificial dataset * pkgdown workflow --------- Co-authored-by: Fersoil <Fersoil> * added STANDARD CURVE type, added option to reverse the xaxis of MFI plot, plots in ggplot2, log scales * docs * plate name detection based on filepath * changed the default log scale into `all` --------- Co-authored-by: Fersoil <Fersoil> * Add tests and setup GHA (#18) * simple README with overview and installation (#7) * website for docs (#8) * add sample vignette and artificial dataset * pkgdown workflow --------- Co-authored-by: Fersoil <Fersoil> * Add .gitignore * Add sample files and adequate tests * Setup package workflow * Style code (GHA) * Export remaining objects * Move dots down * Add missing usage description * Disable lint error * Fix missing import ggplot2 --------- Co-authored-by: Tymoteusz Kwieciński <[email protected]> Co-authored-by: ZetrextJG <[email protected]> * Add dev to GHA for R check and test coverage (#19) * Add codecov (#26) * bug fixes #16, #24 (#32) * simple README with overview and installation (#7) * website for docs (#8) * add sample vignette and artificial dataset * pkgdown workflow --------- Co-authored-by: Fersoil <Fersoil> * bug: standard curve sample type (#13) * simple README with overview and installation (#7) * website for docs (#8) * add sample vignette and artificial dataset * pkgdown workflow --------- Co-authored-by: Fersoil <Fersoil> * added STANDARD CURVE type, added option to reverse the xaxis of MFI plot, plots in ggplot2, log scales * docs * plate name detection based on filepath * changed the default log scale into `all` --------- Co-authored-by: Fersoil <Fersoil> * Add tests and setup GHA (#18) * simple README with overview and installation (#7) * website for docs (#8) * add sample vignette and artificial dataset * pkgdown workflow --------- Co-authored-by: Fersoil <Fersoil> * Add .gitignore * Add sample files and adequate tests * Setup package workflow * Style code (GHA) * Export remaining objects * Move dots down * Add missing usage description * Disable lint error * Fix missing import ggplot2 --------- Co-authored-by: Tymoteusz Kwieciński <[email protected]> Co-authored-by: ZetrextJG <[email protected]> * Add dev to GHA for R check and test coverage (#19) * fixed sample type recognition; added standard curve to summary * updated example script with Covid OISE dataset * updated example script --------- Co-authored-by: Jakub Grzywaczewski <[email protected]> Co-authored-by: ZetrextJG <[email protected]> Co-authored-by: Fersoil <Fersoil> * Covid OISE datasets & external data (#34) * Add covid and external data * Rename file and add a second plate from Covid OISE * description of available datasets --------- Co-authored-by: Fersoil <Fersoil> * Standard curves - normalization & plotting (#36) * simple README with overview and installation (#7) * website for docs (#8) * add sample vignette and artificial dataset * pkgdown workflow --------- Co-authored-by: Fersoil <Fersoil> * added simple nplr model * standard curve as plate attribute; simple plot of fitted model * standard curve model fitting * enchanced standard curve fitting, fixed reading Covid oise files, added docs * expanded example script with Covid oise dataset and curve fitting * predictions in example script * minor fixes of predictions script * covid oise datasets * add `nplr` to `DESCRIPTION` * vignette engine fixes * added `ggplot2` import * error fixes * add imports to vignettes * add docs * CMD check fixes * CMD check warning fixes * correct license formatting * datasets description * add covid oise layout file * restore `qpdf` import --------- Co-authored-by: Fersoil <Fersoil> * Style code (GHA) * update package version * Add R CMD Badge (#46) * Add JakubG to DESCRIPTION (#45) * Add JakubG to DESCRIPTION * Set only one maintainer * Roxygenize with GHA (#43) * add automatic documentation * add github bot as author of the GHA commits * trigger build for docs * Update documentation (GHA) * limit roxygenize on main and dev branch only --------- Co-authored-by: Fersoil <Fersoil> Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com> * DESCRIPTION update (#49) * added myself and bug reports section * typo fixes since there won't be a lot of changes on this branch I think it's a good idea to fix typos here * typo fixes * Update DESCRIPTION --------- Co-authored-by: nizwant <[email protected]> Co-authored-by: Fersoil <Fersoil> * bioconductor compatibility (#47) * add NEWS.md with updates * bioconductor compatibility * documentation according to the bioconductor requirements * remove imports from R code * add PvSTATEM.Rproj to .gitignore * cmd check notes * license according to guidelines * small fixes + docs * typos fixed * missing dependencies * add docs * restored imports to original * remove double BugReports --------- Co-authored-by: Fersoil <Fersoil> Co-authored-by: Mateusz Nizwantowski <[email protected]> * GHA Push token (#50) * Update style.yaml * Add ssh-key to roxygenise GHA * Fix docs (#57) * Remove styler from precommit * Styling changes * Add missing layout file * Fix latex inside docs * Upload complied man and vignettes * Capitalize sentences in docs * Merge latex solutions * added support of documentation for non latex environments * bugfix issue 52 missing plots --------- Co-authored-by: nizwant <[email protected]> * splitting class definitions (#55) * Remove styler from precommit * Styling changes * Add missing layout file * Fix latex inside docs * Upload complied man and vignettes * Capitalize sentences in docs * Merge latex solutions * initialisation of new files * splitting classes into separate files * removed classes file and new documentation * docs for helpers functions * added support of documentation for non latex environments * bugfix issue 52 missing plots * recompiled documentation and small fixes * removed unnecessary example, that causes trouble * recompile documentation * Remove old classes --------- Co-authored-by: ZetrextJG <[email protected]> Co-authored-by: Jakub Grzywaczewski <[email protected]> * Style code (GHA) * Update roxygenize.yaml (#58) * Update standard_curves.R (#59) * Update documentation (GHA) * Dev code cleanup (#60) * docs update * print equation and latex components correctly * initialisation of new files * splitting classes into separate files * removed classes file and new documentation * docs for helpers functions * added support of documentation for non latex environments * bugfix issue 52 missing plots * recompiled documentation and small fixes * removed unnecessary example, that causes trouble * recompile documentation * moved duplicated verbose_cat to helper file * list of colors moved to helpers file * Styling changes --------- Co-authored-by: nizwant <[email protected]> * Feat/refactor (#61) * new plate class * add layout function description * added definition of translate_sample_names_to_sample_types function * Remove old classes * Remove all examples * Builder pattern for Plate. New standard_curve.R implementations (#62) * Remove examples from standard_curves * Use BuilderPattern for plate creation * Implement test for helper functions * Make default unset values nullable * Move the valid checking to non mutable global variables * Change getter method naming * Reimplement first standard curve function with new plate structure * Make dilution encoder more robust. Create better test plate * Add missing docs for is_valid_* * Implement creating the analyte model with new plate structure * Reimplement predict_dilutions * Rewrite the last standard_curve.R function * New parser for xponent and intelliflex files (#44) * Remove examples from standard_curves * Use BuilderPattern for plate creation * Implement test for helper functions * Make default unset values nullable * Move the valid checking to non mutable global variables * Change getter method naming * Reimplement first standard curve function with new plate structure * Make dilution encoder more robust. Create better test plate * Add missing docs for is_valid_* * Implement creating the analyte model with new plate structure * Reimplement predict_dilutions * Rewrite the last standard_curve.R function * Add covid and external data * Rename file and add a second plate from Covid OISE * First version of the new parser * Fix results parsing, add more info to lines * Add eof parser to validate fully parsing a file * Implement backbone for error printing * Adapt all parsers to new error handling * Add external data tests and fix protocol heater * Fix edgecase, rename parser function * Allow changing the separator and encoding of a file * Make join_parsers more readable * Remove na rows * Fix quoting in reading a csv * Change global variable modification * Fix quoting * Implement intelliflex format parsing * Merge inst from dev * Add missing comma * Implement skipping header part of a xPONENT file * Make is_line_blank more robust * Remove the need for a global variable * Fix NAMESPACE * Add missing documentation and export * Remove duplicate code * Rename files to follow the convention * Remove dummy test * Better parser (#65) * Remove examples from standard_curves * Use BuilderPattern for plate creation * Implement test for helper functions * Make default unset values nullable * Move the valid checking to non mutable global variables * Change getter method naming * Reimplement first standard curve function with new plate structure * Make dilution encoder more robust. Create better test plate * Add missing docs for is_valid_* * Implement creating the analyte model with new plate structure * Reimplement predict_dilutions * Rewrite the last standard_curve.R function * Add covid and external data * Rename file and add a second plate from Covid OISE * First version of the new parser * Fix results parsing, add more info to lines * Add eof parser to validate fully parsing a file * Implement backbone for error printing * Adapt all parsers to new error handling * Add external data tests and fix protocol heater * Fix edgecase, rename parser function * Allow changing the separator and encoding of a file * Make join_parsers more readable * Remove na rows * Fix quoting in reading a csv * Change global variable modification * Fix quoting * Implement intelliflex format parsing * Merge inst from dev * Add missing comma * Implement skipping header part of a xPONENT file * Make is_line_blank more robust * Remove the need for a global variable * Fix NAMESPACE * Add missing documentation and export * Remove duplicate code * Rename files to follow the convention * Remove dummy test * Layout parser (#64) * Move tymek implementation * Generate a real csv file for tests * Implement the layout parser * Add parser documentation * Name form luminex of layout file to sample type (#66) * temporary place to develop and test function to derive type and dilution * removed deriving dilutions in this function * Refactor derive_sample_type function to handle vector of strings * rename passed arguments to plural * insert new function implementation into code base * remove tmp file * tests of deriving type from names * positive control more generic recognition and compatibility with newer R versions * Make roxygen happy * Parser (#67) * Base of the parser implementation * Create parser integration tests * Remove intermediate functions from user access * Add R6 to class import * Integrate parser with validated input * Fix typo * Make R6 only importFrom * Blank adjustment (#68) * Base of the parser implementation * Create parser integration tests * Remove intermediate functions from user access * Integrate parser with validated input * Fix typo * Reimplement blank-adjustment * Fix parsing dilutions (#70) * fixed log scale for plots #72 (#75) Co-authored-by: Fersoil <Fersoil> * Implement boxplot for MFI (#69) * Implement boxplot for MFI * Reimplement mfi plot for test samples * Encapsulate model (#76) * Reimplement standard curve model WIP * Fix model plot_data sequence * Fix indentation * Make roxygen happy * Reimplement standard curve plotting * Rename SCModel to Model * Add docs for init, plot_data, predict method for Model * Move top bottom asymptote to active fields * Add missing docs for generic functions * Fix typo * Add print method and examples * Rename model to classes-model * Move replicated code to a private function * Rename plot_data to get_plot_data * Fix typo * Improve performace of a hot loop in the xponent parser (#82) * Improve performace of a hot loop in the xponent parser * fixed quotation marks --------- Co-authored-by: Tymoteusz Kwieciński <[email protected]> * Dilution detection (#80) * updated the extraction of dilutions * renamed setters for dilutions and types as `set_*` instead of `extract_*`; added active field for converting the layout into the vector; verbosity; error fixes * fixed errors; added warnings * added tests, verbosity parameter to the reading function * update docs * fixes of indicated bugs --------- Co-authored-by: Fersoil <Fersoil> * Add more information to standard curve plots (#87) * Improve performace of a hot loop in the xponent parser * Allow extracting data for all analytes * Model: Allow setting min and max mfi for scaling * Improve the quality of the sc plots * Model: Adjust lower bound * fix typos * plot labeling * additional plot parameters --------- Co-authored-by: Tymoteusz Kwieciński <[email protected]> Co-authored-by: Fersoil <Fersoil> * validation and docs after refactor (#85) * docs and validation for `Plate` class * additional documentation - better display of available sample and data types * typos * reuse the data types from plate class * added `...` documentation * minor docs changes * verbose options for main reading function * suppress verbosity during tests * add sample example script * consistency in naming the function parameters `analyte` -> `analyte_name` * removed doubled output during plate creating * updated the vignette with example script * set `plate_name` as the filename, the old plate name is now called `batch_name` #77 * added tests for #77 * changes made according to the comments --------- Co-authored-by: Fersoil <Fersoil> * More detailed plate summary (#84) * copying the old summary method * add S3 style summary function * extensive summary * S3 method proper implementation --------- Co-authored-by: nizwant <[email protected]> Co-authored-by: Fersoil <Fersoil> * plots of plate - counts and layout (#71) * initial plot_plate functionality * code refactoring * creating a function out of code for plotting * handle plotting numbers in wells and finally path to image that works * handling errors * install packages moved to description * plot counts * plot layout * Add dependencies properly and remove code use for tests * documentation for plot plate functionalities * new colours and refactoring * added scaling of numbers size * bold title font and slight tweaks to points size * finally legend (it was a pain) * updated docs and stylistic changes * examples in docs * plate as an argument * bugfix * count plot is working * layout is working * add examples to plot layout and plot count * rerun roxygen * fixes pt.1 * fixes pt.2 * docs update * better documentation * better documentation pt.2 * automatic dosc generation * fixes of documentation * Plate layout (#94) * sample names from layout * simple layout validation * some simple docs --------- Co-authored-by: Fersoil <Fersoil> * feat: model carrying more info (#92) * add analyte into the model * `plot_standard_curve_with_model` adapted to the changes * fix error #90 --------- Co-authored-by: Fersoil <Fersoil> * Our plots vignette (#97) * introduction to our plots * plot layout * plot counts description * remove ggplot dependency * renaming of plots file * mfi * roxygen update * change to valid antibody and bug fix * standard curve without model * plot with model pl1 * plot with model pt2 * typos pt1 * typos pt2 * typos pt3 * error fixes: removed `dilutions_from` parmeter * error fixes: fixed the `plot_standard_curve_analyte` syntax in tests * fix dependencies * fix errors: examples in internal functions * supplementing the documentation * fix errors: internal function in docs examples * added plate tests * added tests * typo fixes * tests for `plot_plate` removed `require` statement --------- Co-authored-by: nizwant <[email protected]> Co-authored-by: Tymoteusz Kwieciński <[email protected]> Co-authored-by: Fersoil <Fersoil> * Style code (GHA) * Update documentation (GHA) * Display outliers only for boxplot (#103) * Inform the user about summary generic in vignettes (#105) * Alternate the outlier label to avoid overcrowding (#104) * Display outliers only for boxplot * Alternate the outlier label to avoid overcrowding --------- Co-authored-by: Mateusz Nizwantowski <[email protected]> * Add ggrepel to mfi plot (#106) * remove overlap * add dependencies * Style code (GHA) * New blank adjustment (#102) * Clamp method implementation * Reimplement blank adjustment * Small visual fix for vignettes * added new blank adjustment test * test fixes * Update R/classes-plate.R Co-authored-by: Tymoteusz Kwieciński <[email protected]> --------- Co-authored-by: Fersoil <Fersoil> Co-authored-by: Tymoteusz Kwieciński <[email protected]> * Style code (GHA) * Update documentation (GHA) * Fix: layout indeed can be longer the samples (#109) * Fix: layout indeed can be longer the samples * Update docs * Process plate function (#110) * Fix: layout indeed can be longer the samples * Update docs * Basic implementation of process plate function * Make plot_layout and plot_counts look a little better in vignettes (#101) * Make plot_layout and plot_counts look a little better in vignetts * fixed the plate plot generation * typo fix --------- Co-authored-by: Fersoil <Fersoil> * Style code (GHA) * Release 0.0.3 (#112) * news and package version update * fix #108 * tests for #108 fix * fix typos --------- Co-authored-by: Fersoil <Fersoil> * Style code (GHA) * Remove todo from vignette (#115) * correct mistakes in vignettes * styling * grammar mistakes * how to link your own files --------- Co-authored-by: Tymoteusz Kwieciński <[email protected]> --------- Co-authored-by: Jakub Grzywaczewski <[email protected]> Co-authored-by: ZetrextJG <[email protected]> Co-authored-by: Fersoil <Fersoil> Co-authored-by: Fersoil <[email protected]> Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Co-authored-by: nizwant <[email protected]> Co-authored-by: ZetrextJG <[email protected]>
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