Olink Analyze 3.3.0

Minor Changes

Support for additional versions of Olink data - Read_NPX now supports a wider range of Olink data types (@AskPascal, @kathy-nevola, #207, #208, #211, #216)
Automatic support for normalizing 2 datasets with different column configurations - olink_normalization will now automatically add missing columns to datasets (filled NA) to allow data with different configurations to be more easily normalized together (@kathy-nevola, #212)
Automatic checking that datasets used the same normalization method before bridging - Datasets that were normalized with different methods (different values in normalization column) will now warn before performing normalization (@klevdiamanti, #210)

Data with ‘#’ in SampleID column is now supported (@AskPascal, #208)
PCA can now be generated when indices are not consistent across SampleIDs (@amrita-kar, #206)

remove www. from links in vignette to prevent rerouting of URL (@kathy-nevola, #188)
update set_plot_theme() to use linewidth instead of size per ggplot2 3.4

Addition of functions to perform Uniform Manifold Approximation and Projection (UMAP) dimensional reduction and plots (@simfor, #139)
Add additional install methods to Readme (@AskPascal, #153)
ggrepel can now be disabled when outlier lines are present in the PCA plot (@klevdiamanti, #158)
Long running unit tests are now skipped on CRAN (@AskPascal, #163)
Internal functions were added to read_NPX to support future development (@klevdiamanti, #167)
CI workflows were refactored to utilize external actions (@AskPascal, #169)
Read_NPX will now warn the user when NAs are detected in the NPX column (@AskPascal, #170)
Friedman test interface and documentation was updated to be more intuitive (@boxizhang, #171)

Pathway enrichment p-values are now in the correct order when plotting (@klevdiamanti, #164)
PCAs now behave the same with any locale (@AskPascal, #173)
Read_NPX now accepts either Panel_Version or Panel_Lot_Nr in input files (@klevdiamanti, #156)
Assays that only have NPX = NA will now be excluded from all analyses and figures (@simfor, @kathy-nevola, @AskPascal, #176)
Refactor code to use tidyselect::all_of() in recommended way (@AskPascal, #177)
vdiffr based unit tests were reactivated (@AskPascal, #172)

Non-parametric functions are now available (@boxizhang, #114, #142)
Updated installation instructions to reflect CRAN acceptance (@kathy-nevola, #107)
Zipped files from MyData can now be used as input for read_NPX (@klevdiamanti, #115)
LME and ANOVA formulas can now be customized (@jrguess, #120)
Pathway enrichment functions and visualizations are now available (@kathy-nevola, #125)
Heatmaps can now be generated (@Orbmac, $127)
olink_boxplot function now has significance bars and stars (@boxizhang, #132)
PCA preprocessing was moved to internal function (@simfor, #133)
olink_plate_randomizer will now return a warning if there are duplicate SampleIDs or if SubjectColumn is missing (@kristianHoden, #146)
olink_plate_randomizer can now keep studies together on plates (@kristianHoden, #146)
Added Masoumeh Sheikhi and Boxi Zhang as authors
Added Kristian Hodén as contributor

olink_pca_plot by Panel will now show correct colors when a variable is missing (@MasoumehSheikhi, Issue #117, Commit 0f2f157)
olink_ttest will now return a warning message if an assay has less than 2 datapoints in a group. (@marisand, #110)
LMER class is now checked using inherits (@MasoumehSheikhi, #134)
License was corrected to AGPL-3 (@Orbmac, #138)
Correct output type of olink_dist_plot in vignette to ggplot object (@kathy-nevola, Issue #112, #141)
Previously called “intensity normalization” has been clarified as a special type of subset normalization and an example has been added to the documentation and vignette (@Orbmac, #144)

displayPlateDistributions and displayPlateLayout names were updated to olink_displayPlateDistributions and olink_displayPlateLayout (@simfor, #98)

Update CI to Ubuntu 20.04 (@AskPascal, #97)
olink_bridgeselector will now give an error if less than n (number of) bridge samples can be selected based on set sampleMissingFreq (@marisand, #100)
update return value documentation for all functions to specify columns and class of output (@kathy-nevola, #102)
replaced or removed cat/print with message/stop so messages printed to the console can be suppressed (@jrguess, #103)

fixed spelling mistakes in documentation (@kathy-nevola, #92)
updated DESCRIPTION to fit CRAN specification (@kathy-nevola, #94)
change T/F to TRUE/FALSE for stability (@AskPascal, #96)
updated documentation to olink_plate_randomizer, olink_displayPlateDistributions and olink_displayPlateLayout to link related functions and clarify olink_plate_randomizer documentation (@simfor, #98)
fixed keywords in documentation (@kathy-nevola, #99)

Package is in the process of being submitted to CRAN
Added ability to prevent OlinkAnalyze from loading fonts and setting to themes (@OlaCaster, #73)
Decreased the size of npx_data1 and npx_data2 to 2 panels instead of 12 (@kathy-nevola, #76)
Updates to the olink_qc_plot and olink_pca_plot functions (@simfor, #78)

Moved NEWS.md to correct level (@kathy-nevola, #74)
Added cran-comments.md file to document Notes for CRAN submission (@kathy-nevola, #74)
Update Vignette to reflect new functionality (@kathy-nevola, #78)

DESCRIPTION file updated to include all authors and maintainers (@kathy-nevola, #66)
Unit testing was added (@marisand, @simfor, #65, #55, #47)
Continuous Integration (CI) was added (@AskPascal, #57, #53, #40, #31)
read_NPX now converts Panel Names to Sentence case except Roman Numerals (@kathy-nevola, #44)
Output order of olink_bridgeselector() is now randomized (@marisand, #60)
PlateSize argument was added to displayPlateLayout() and olink_plate_randomizer for T48 and T96. Hardcoded sizes have been removed. (@marisand, #47)
Changed olink_pal() to have gray instead of light blue (@marisand, #22)

set_plot_theme() will now load Swedish Gothic Thin if available on all OS (@marisand, @AskPascal, #70, #39)
Help documentation was updated to correct typos and clarify notation for ANOVA and LME models (@kathy-nevola, @marisand,@AskPascal #67, #33, #37)
Fix olink_dist_plot() from showing multiple bars when sample has QC warning in some assays (@marisand, @AskPascal, #64)
Fix olink_qc_plot() from showing multiple points/labels when sample has QC warning in some assays (@marisand, @AskPascal, #63)
Panel names in npx_data1 and npx_data2 were fixed to match new read_NPX() formatting (@kathy-nevola, #62)
olink_bridgeselector() QC warning filtering changed to match olink_qc_plot() and olink_dist_plot() (@marisand, @AskPascal, #61)
global variables are now specified (@kathy-nevola, #45)
Function documentation updated to remove notes on R CMD check (@kathy-nevola, #39)
Fix summary casting “tukey” to “sidak” adjustment warning in olink_anova_posthoc() and olink_lmer_posthoc() functions (@marisand, #38)
Update functions to import selectively (@kathy-nevola, @Orbmac, @AskPascal, @marisand, #21, #20, #19, #18, #15, #29)
Fix guides size argument in olink_pca_plot() (#17) (@AskPascal, #24)