From d30b2c07b9011f3325493fc9b00752fd0e69a71a Mon Sep 17 00:00:00 2001 From: Gene233 <44050457+Gene233@users.noreply.github.com> Date: Fri, 29 Mar 2024 11:42:47 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20DavisLab?= =?UTF-8?q?oratory/smartid@27f0ddc92122b9ca82c25971a126c9ae246fa7c1=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/smartid_Demo.html | 112 ++++++++++-------- .../figure-html/unnamed-chunk-6-1.png | Bin 51216 -> 47639 bytes news/index.html | 2 +- pkgdown.yml | 2 +- reference/scale_mgm.html | 7 +- 5 files changed, 69 insertions(+), 54 deletions(-) diff --git a/articles/smartid_Demo.html b/articles/smartid_Demo.html index d0eae4b..599cb7d 100644 --- a/articles/smartid_Demo.html +++ b/articles/smartid_Demo.html @@ -270,7 +270,7 @@
-ggplot(data.frame(
- "Gene76" = slot(data_sim, "metadata")$tf["Gene76", ],
- Group = data_sim$Group
-)) +
- geom_violin(aes(x = Group, y = Gene76, fill = Group)) +
- theme_bw()
sin_score_boxplot(
+ metadata(data_sim)$tf,
+ features = "Gene76",
+ ref.group = "Group2",
+ label = data_sim$Group
+)
+#> Warning: `add_rownames()` was deprecated in dplyr 1.0.0.
+#> ℹ Please use `tibble::rownames_to_column()` instead.
+#> ℹ The deprecated feature was likely used in the smartid package.
+#> Please report the issue at
+#> <https://github.com/DavisLaboratory/smartid/issues>.
+#> This warning is displayed once every 8 hours.
+#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
+#> generated.
@@ -426,10 +434,11 @@
. Different fromMarker Selectionmclust
markers_mixmdl()
,markers_mclust()
doesn’t need a pre-defined number of -components (which is 3 inmarkers_mixmdl()
), instead, it -will select the number of components by searching a series of potential -numbers. This method is sometimes more robust than -markers_mixmdl()
. +components (which is default 3 inmarkers_mixmdl()
), +instead, it will select the number of components by searching a series +of potential numbers. This method is sometimes more robust than +markers_mixmdl()
but will also take longer running +time.Similarly, this method also allows to plot the mixture distribution for each component, but separately.
+#> [29] BiocParallel_1.37.1 broom_1.0.5 +#> [31] irlba_2.3.5.1 parallel_4.4.0 +#> [33] R6_2.5.1 bslib_0.7.0 +#> [35] stringi_1.8.3 car_3.1-2 +#> [37] jquerylib_0.1.4 Rcpp_1.0.12 +#> [39] bookdown_0.38 knitr_1.45 +#> [41] mixtools_2.0.0 splines_4.4.0 +#> [43] Matrix_1.7-0 tidyselect_1.2.1 +#> [45] abind_1.4-5 yaml_2.3.8 +#> [47] viridis_0.6.5 codetools_0.2-19 +#> [49] plyr_1.8.9 lattice_0.22-6 +#> [51] tibble_3.2.1 withr_3.0.0 +#> [53] evaluate_0.23 survival_3.5-8 +#> [55] desc_1.4.3 mclust_6.1 +#> [57] kernlab_0.9-32 pillar_1.9.0 +#> [59] BiocManager_1.30.22 ggpubr_0.6.0 +#> [61] carData_3.0-5 janeaustenr_1.0.0 +#> [63] checkmate_2.3.1 plotly_4.10.4 +#> [65] generics_0.1.3 RCurl_1.98-1.14 +#> [67] sparseMatrixStats_1.15.0 munsell_0.5.0 +#> [69] scales_1.3.0 glue_1.7.0 +#> [71] lazyeval_0.2.2 tools_4.4.0 +#> [73] data.table_1.15.2 BiocNeighbors_1.21.2 +#> [75] tokenizers_0.3.0 ScaledMatrix_1.11.1 +#> [77] ggsignif_0.6.4 locfit_1.5-9.9 +#> [79] fs_1.6.3 grid_4.4.0 +#> [81] tidyr_1.3.1 colorspace_2.1-0 +#> [83] nlme_3.1-164 GenomeInfoDbData_1.2.12 +#> [85] beeswarm_0.4.0 BiocSingular_1.19.0 +#> [87] vipor_0.4.7 cli_3.6.2 +#> [89] rsvd_1.0.5 textshaping_0.3.7 +#> [91] fansi_1.0.6 segmented_2.0-3 +#> [93] S4Arrays_1.3.6 viridisLite_0.4.2 +#> [95] dplyr_1.1.4 gtable_0.3.4 +#> [97] rstatix_0.7.2 sass_0.4.9 +#> [99] digest_0.6.35 SparseArray_1.3.4 +#> [101] ggrepel_0.9.5 htmlwidgets_1.6.4 +#> [103] farver_2.1.1 memoise_2.0.1 +#> [105] htmltools_0.5.8 pkgdown_2.0.7 +#> [107] lifecycle_1.0.4 httr_1.4.7 +#> [109] MASS_7.3-60.2@@ -482,7 +491,7 @@Score Samples ) ) #> user system elapsed -#> 0.170 0.028 0.198 +#> 0.178 0.020 0.198 ## new score is saved and tf,idf,iae all updated assays(data_sim) @@ -584,44 +593,47 @@
SessionInfo#> [23] cachem_1.0.8 beachmat_2.19.2 #> [25] jsonlite_1.8.8 SnowballC_0.7.1 #> [27] highr_0.10 DelayedArray_0.29.9 -#> [29] BiocParallel_1.37.1 irlba_2.3.5.1 -#> [31] parallel_4.4.0 R6_2.5.1 -#> [33] bslib_0.7.0 stringi_1.8.3 -#> [35] jquerylib_0.1.4 Rcpp_1.0.12 -#> [37] bookdown_0.38 knitr_1.45 -#> [39] mixtools_2.0.0 splines_4.4.0 -#> [41] Matrix_1.7-0 tidyselect_1.2.1 -#> [43] abind_1.4-5 yaml_2.3.8 -#> [45] viridis_0.6.5 codetools_0.2-19 -#> [47] plyr_1.8.9 lattice_0.22-6 -#> [49] tibble_3.2.1 withr_3.0.0 -#> [51] evaluate_0.23 survival_3.5-8 -#> [53] desc_1.4.3 mclust_6.1 -#> [55] kernlab_0.9-32 pillar_1.9.0 -#> [57] BiocManager_1.30.22 janeaustenr_1.0.0 -#> [59] checkmate_2.3.1 plotly_4.10.4 -#> [61] generics_0.1.3 RCurl_1.98-1.14 -#> [63] sparseMatrixStats_1.15.0 munsell_0.5.0 -#> [65] scales_1.3.0 glue_1.7.0 -#> [67] lazyeval_0.2.2 tools_4.4.0 -#> [69] data.table_1.15.2 BiocNeighbors_1.21.2 -#> [71] tokenizers_0.3.0 ScaledMatrix_1.11.1 -#> [73] locfit_1.5-9.9 fs_1.6.3 -#> [75] grid_4.4.0 tidyr_1.3.1 -#> [77] colorspace_2.1-0 nlme_3.1-164 -#> [79] GenomeInfoDbData_1.2.12 beeswarm_0.4.0 -#> [81] BiocSingular_1.19.0 vipor_0.4.7 -#> [83] cli_3.6.2 rsvd_1.0.5 -#> [85] textshaping_0.3.7 fansi_1.0.6 -#> [87] segmented_2.0-3 S4Arrays_1.3.6 -#> [89] viridisLite_0.4.2 dplyr_1.1.4 -#> [91] gtable_0.3.4 sass_0.4.9 -#> [93] digest_0.6.35 SparseArray_1.3.4 -#> [95] ggrepel_0.9.5 htmlwidgets_1.6.4 -#> [97] farver_2.1.1 memoise_2.0.1 -#> [99] htmltools_0.5.8 pkgdown_2.0.7 -#> [101] lifecycle_1.0.4 httr_1.4.7 -#> [103] MASS_7.3-60.2
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