diff --git a/doc/.~lock.ici_kt_manuscript.docx# b/doc/.~lock.ici_kt_manuscript.docx# new file mode 100644 index 0000000..4150f6b --- /dev/null +++ b/doc/.~lock.ici_kt_manuscript.docx# @@ -0,0 +1 @@ +,rmflight,pop-os.localdomain,01.03.2022 08:48,file:///home/rmflight/.config/libreoffice/4; \ No newline at end of file diff --git a/doc/ici_kt_manuscript.Rmd b/doc/ici_kt_manuscript.Rmd index b977cf9..dd1c7b8 100644 --- a/doc/ici_kt_manuscript.Rmd +++ b/doc/ici_kt_manuscript.Rmd @@ -103,7 +103,7 @@ We examine the effect of missing values on simulated data, comparing our informa We also evaluate the ability of ICI-Kt to capture outlier samples using three different RNA-seq datasets and comparing to a standard method using Pearson correlation. Finally, we examine the ability to recapitulate ICI-Kt correlation values calculated on a large feature omics data set using feature subsets, which is useful when the execution time of very large feature data sets becomes computationally prohibitive. -All of the code used for this manuscript is available on figshare [@flightManuscriptICIKendallTau2022]. +All of the code used for this manuscript is available on zenodo [@flightManuscriptICIKendallTau2022]. ## Methods @@ -190,7 +190,7 @@ In comparison to directly counting the concordant and discordant pairs, some of Therefore, we used 64 bit integers and floats where necessary in the *Rcpp* code. C++ (via *Rcpp* [@eddelbuettel_rcppseamless_2011; @eddelbuettel_seamlessbook_2013; @eddelbuettel_extendingrcpp_2018]) and R code implementations are in the src/kendallc.cpp and R/kendalltau.R files of the ICIKendallTau R package, hosted at https://github.com/MoseleyBioinformaticsLab/ICIKendallTau. -The version of the package used in this manuscript is available on figshare [@flightICIKendallTau2022]. +The version of the package used in this manuscript is available on zenodo [@flightICIKendallTau2022]. When a large number of samples need to be compared, it may be useful to split the comparisons across compute instances (across hyperthreaded cores, physical cores, or physical compute nodes). The *furrr* R package makes the definition of compute clusters easy [@vaughanFurrrApplyMapping2021]. @@ -406,7 +406,6 @@ figure_count$increment("leftcensored") ``` ```{r leftcensored, fig.height = 8, fig.width = 8, dn_id = figure_count} -figure_count$increment("f_leftcensored") loadd(left_censored_cor) left_censored_cor = left_censored_cor %>% dplyr::mutate(which2 = dplyr::case_when( diff --git a/doc/ici_kt_manuscript.docx b/doc/ici_kt_manuscript.docx index 2af5582..0a4fe1e 100644 Binary files a/doc/ici_kt_manuscript.docx and b/doc/ici_kt_manuscript.docx differ diff --git a/doc/ici_kt_manuscript_files/figure-docx/Figure_11_pearson_nolog-1.png b/doc/ici_kt_manuscript_files/figure-docx/Figure_10_pearson_nolog-1.png similarity index 100% rename from doc/ici_kt_manuscript_files/figure-docx/Figure_11_pearson_nolog-1.png rename to doc/ici_kt_manuscript_files/figure-docx/Figure_10_pearson_nolog-1.png diff --git a/doc/ici_kt_manuscript_files/figure-docx/Figure_12_pcavardifference-1.png b/doc/ici_kt_manuscript_files/figure-docx/Figure_11_pcavardifference-1.png similarity index 100% rename from doc/ici_kt_manuscript_files/figure-docx/Figure_12_pcavardifference-1.png rename to doc/ici_kt_manuscript_files/figure-docx/Figure_11_pcavardifference-1.png diff --git a/doc/ici_kt_manuscript_files/figure-docx/Figure_13_pcaeval-1.png b/doc/ici_kt_manuscript_files/figure-docx/Figure_12_pcaeval-1.png similarity index 100% rename from doc/ici_kt_manuscript_files/figure-docx/Figure_13_pcaeval-1.png rename to doc/ici_kt_manuscript_files/figure-docx/Figure_12_pcaeval-1.png diff --git a/doc/ici_kt_manuscript_files/figure-docx/Figure_5_singleperf-1.png b/doc/ici_kt_manuscript_files/figure-docx/Figure_4_singleperf-1.png similarity index 100% rename from doc/ici_kt_manuscript_files/figure-docx/Figure_5_singleperf-1.png rename to doc/ici_kt_manuscript_files/figure-docx/Figure_4_singleperf-1.png diff --git a/doc/ici_kt_manuscript_files/figure-docx/Figure_6_multiperformance-1.png b/doc/ici_kt_manuscript_files/figure-docx/Figure_5_multiperformance-1.png similarity index 100% rename from doc/ici_kt_manuscript_files/figure-docx/Figure_6_multiperformance-1.png rename to doc/ici_kt_manuscript_files/figure-docx/Figure_5_multiperformance-1.png diff --git a/doc/ici_kt_manuscript_files/figure-docx/Figure_7_yeast_outliers-1.png b/doc/ici_kt_manuscript_files/figure-docx/Figure_6_yeast_outliers-1.png similarity index 100% rename from doc/ici_kt_manuscript_files/figure-docx/Figure_7_yeast_outliers-1.png rename to doc/ici_kt_manuscript_files/figure-docx/Figure_6_yeast_outliers-1.png diff --git a/doc/ici_kt_manuscript_files/figure-docx/Figure_8_brainson_outliers-1.png b/doc/ici_kt_manuscript_files/figure-docx/Figure_7_brainson_outliers-1.png similarity index 100% rename from doc/ici_kt_manuscript_files/figure-docx/Figure_8_brainson_outliers-1.png rename to doc/ici_kt_manuscript_files/figure-docx/Figure_7_brainson_outliers-1.png diff --git a/doc/ici_kt_manuscript_files/figure-docx/Figure_9_adeno_outliers-1.png b/doc/ici_kt_manuscript_files/figure-docx/Figure_8_adeno_outliers-1.png similarity index 100% rename from doc/ici_kt_manuscript_files/figure-docx/Figure_9_adeno_outliers-1.png rename to doc/ici_kt_manuscript_files/figure-docx/Figure_8_adeno_outliers-1.png diff --git a/doc/ici_kt_manuscript_files/figure-docx/Figure_10_icisubsampling-1.png b/doc/ici_kt_manuscript_files/figure-docx/Figure_9_icisubsampling-1.png similarity index 100% rename from doc/ici_kt_manuscript_files/figure-docx/Figure_10_icisubsampling-1.png rename to doc/ici_kt_manuscript_files/figure-docx/Figure_9_icisubsampling-1.png diff --git a/doc/ici_kt_manuscript_files/figure-docx/brainsonseq_outliers-1.png b/doc/ici_kt_manuscript_files/figure-docx/brainsonseq_outliers-1.png deleted file mode 100644 index 439c684..0000000 Binary files a/doc/ici_kt_manuscript_files/figure-docx/brainsonseq_outliers-1.png and /dev/null differ diff --git a/doc/icikt_references.json b/doc/icikt_references.json index 9290abe..8bc90d7 100644 --- a/doc/icikt_references.json +++ b/doc/icikt_references.json @@ -2041,7 +2041,7 @@ "type": "article", "abstract": "ICIKendallTau version used in the manuscript Information-Content-Informed Kendall-tau Correlation: Utilizing Missing Values Robert M Flight, Praneeth S Bhatt, Hunter NB Moseley", "title": "ICIKendallTau", - "URL": "https://figshare.com/articles/software/ICIKendallTau/19192886/1", + "URL": "https://doi.org/10.5281/zenodo.6311002", "author": [ { "family": "Flight", @@ -2066,7 +2066,7 @@ "id": "flightManuscriptICIKendallTau2022", "type": "article", "title": "manuscript.ICIKendallTau", - "URL": "https://dx.doi.org/10.6084/m9.figshare.19196645", + "URL": "https://dx.doi.org/10.5281/zenodo.6309187", "author": [ { "family": "Flight",