diff --git a/404.html b/404.html index dece77f..4b51e36 100644 --- a/404.html +++ b/404.html @@ -32,7 +32,7 @@ MicrobiomeBenchmarkDataAnalyses - 0.99.11 + 0.99.12 diff --git a/LICENSE-text.html b/LICENSE-text.html index 69ca8b3..0d3b856 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -17,7 +17,7 @@ MicrobiomeBenchmarkDataAnalyses - 0.99.11 + 0.99.12 diff --git a/LICENSE.html b/LICENSE.html index 832e1d0..fddb811 100644 --- a/LICENSE.html +++ b/LICENSE.html @@ -17,7 +17,7 @@ MicrobiomeBenchmarkDataAnalyses - 0.99.11 + 0.99.12 diff --git a/articles/HMP_2012_16S_gingival_V13.html b/articles/HMP_2012_16S_gingival_V13.html index 98c58f9..7968c90 100644 --- a/articles/HMP_2012_16S_gingival_V13.html +++ b/articles/HMP_2012_16S_gingival_V13.html @@ -32,7 +32,7 @@ MicrobiomeBenchmarkDataAnalyses - 0.99.11 + 0.99.12 @@ -333,7 +333,7 @@

Differential abundance analysis}) tim #> user system elapsed -#> 100.118 19.847 100.800 +#> 100.111 19.823 100.903

Enrichment analysis @@ -437,7 +437,7 @@

Session Info#> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Etc/UTC -#> date 2024-12-04 +#> date 2024-12-05 #> pandoc 3.5 @ /usr/bin/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── @@ -536,7 +536,7 @@

Session Info#> genefilter 1.88.0 2024-10-29 [1] Bioconductor 3.20 (R 4.4.2) #> generics 0.1.3 2022-07-05 [1] RSPM (R 4.4.0) #> GenomeInfoDb * 1.42.1 2024-11-28 [1] Bioconductor 3.20 (R 4.4.2) -#> GenomeInfoDbData 1.2.13 2024-12-04 [1] Bioconductor +#> GenomeInfoDbData 1.2.13 2024-12-05 [1] Bioconductor #> GenomicRanges * 1.58.0 2024-10-29 [1] Bioconductor 3.20 (R 4.4.2) #> getopt 1.20.4 2023-10-01 [1] RSPM (R 4.4.0) #> ggbeeswarm 0.7.2 2023-04-29 [1] RSPM (R 4.4.0) @@ -618,7 +618,7 @@

Session Info#> mice 3.17.0 2024-11-27 [1] RSPM (R 4.4.0) #> microbiome 1.28.0 2024-10-29 [1] Bioconductor 3.20 (R 4.4.2) #> MicrobiomeBenchmarkData * 1.8.0 2024-10-31 [1] Bioconductor 3.20 (R 4.4.2) -#> MicrobiomeBenchmarkDataAnalyses * 0.99.11 2024-12-04 [1] local +#> MicrobiomeBenchmarkDataAnalyses * 0.99.12 2024-12-05 [1] local #> MicrobiomeStat 1.2 2024-04-01 [1] RSPM (R 4.4.0) #> mime 0.12 2021-09-28 [1] RSPM (R 4.4.0) #> miniUI 0.1.1.1 2018-05-18 [1] RSPM (R 4.4.0) @@ -772,7 +772,7 @@

Session Info#> yulab.utils 0.1.8 2024-11-07 [1] RSPM (R 4.4.0) #> zCompositions 1.5.0-4 2024-06-19 [1] RSPM (R 4.4.0) #> zinbwave 1.28.0 2024-10-29 [1] Bioconductor 3.20 (R 4.4.2) -#> ZINQ 2.0 2024-12-04 [1] Github (wdl2459/ZINQ-v2@40391a6) +#> ZINQ 2.0 2024-12-05 [1] Github (wdl2459/ZINQ-v2@40391a6) #> zlibbioc 1.52.0 2024-10-29 [1] Bioconductor 3.20 (R 4.4.2) #> zoo 1.8-12 2023-04-13 [1] RSPM (R 4.4.0) #> diff --git a/articles/HMP_2012_16S_gingival_V35.html b/articles/HMP_2012_16S_gingival_V35.html index d0d9ccf..ef63d17 100644 --- a/articles/HMP_2012_16S_gingival_V35.html +++ b/articles/HMP_2012_16S_gingival_V35.html @@ -32,7 +32,7 @@ MicrobiomeBenchmarkDataAnalyses - 0.99.11 + 0.99.12

@@ -334,7 +334,7 @@

Differential abundance analysis}) tim #> user system elapsed -#> 131.715 26.928 132.169 +#> 132.915 26.949 133.308

Enrichment analysis @@ -591,7 +591,7 @@

Session Info#> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Etc/UTC -#> date 2024-12-04 +#> date 2024-12-05 #> pandoc 3.5 @ /usr/bin/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── @@ -692,7 +692,7 @@

Session Info#> genefilter 1.88.0 2024-10-29 [1] Bioconductor 3.20 (R 4.4.2) #> generics 0.1.3 2022-07-05 [1] RSPM (R 4.4.0) #> GenomeInfoDb * 1.42.1 2024-11-28 [1] Bioconductor 3.20 (R 4.4.2) -#> GenomeInfoDbData 1.2.13 2024-12-04 [1] Bioconductor +#> GenomeInfoDbData 1.2.13 2024-12-05 [1] Bioconductor #> GenomicRanges * 1.58.0 2024-10-29 [1] Bioconductor 3.20 (R 4.4.2) #> getopt 1.20.4 2023-10-01 [1] RSPM (R 4.4.0) #> ggbeeswarm 0.7.2 2023-04-29 [1] RSPM (R 4.4.0) @@ -776,7 +776,7 @@

Session Info#> mice 3.17.0 2024-11-27 [1] RSPM (R 4.4.0) #> microbiome 1.28.0 2024-10-29 [1] Bioconductor 3.20 (R 4.4.2) #> MicrobiomeBenchmarkData * 1.8.0 2024-10-31 [1] Bioconductor 3.20 (R 4.4.2) -#> MicrobiomeBenchmarkDataAnalyses * 0.99.11 2024-12-04 [1] local +#> MicrobiomeBenchmarkDataAnalyses * 0.99.12 2024-12-05 [1] local #> MicrobiomeStat 1.2 2024-04-01 [1] RSPM (R 4.4.0) #> mime 0.12 2021-09-28 [1] RSPM (R 4.4.0) #> miniUI 0.1.1.1 2018-05-18 [1] RSPM (R 4.4.0) @@ -931,7 +931,7 @@

Session Info#> yulab.utils 0.1.8 2024-11-07 [1] RSPM (R 4.4.0) #> zCompositions 1.5.0-4 2024-06-19 [1] RSPM (R 4.4.0) #> zinbwave 1.28.0 2024-10-29 [1] Bioconductor 3.20 (R 4.4.2) -#> ZINQ 2.0 2024-12-04 [1] Github (wdl2459/ZINQ-v2@40391a6) +#> ZINQ 2.0 2024-12-05 [1] Github (wdl2459/ZINQ-v2@40391a6) #> zlibbioc 1.52.0 2024-10-29 [1] Bioconductor 3.20 (R 4.4.2) #> zoo 1.8-12 2023-04-13 [1] RSPM (R 4.4.0) #> diff --git a/articles/HMP_2012_16S_gingival_V35_subset.html b/articles/HMP_2012_16S_gingival_V35_subset.html index 9004fc1..63cfbe1 100644 --- a/articles/HMP_2012_16S_gingival_V35_subset.html +++ b/articles/HMP_2012_16S_gingival_V35_subset.html @@ -32,7 +32,7 @@ MicrobiomeBenchmarkDataAnalyses - 0.99.11 + 0.99.12

@@ -223,7 +223,7 @@

Run DA }) tim 
##    user  system elapsed 
-##  48.049   0.508  48.291
+## 48.440 0.520 48.687

Enrichment @@ -323,7 +323,7 @@

Session info## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz Etc/UTC -## date 2024-12-04 +## date 2024-12-05 ## pandoc 3.5 @ /usr/bin/ (via rmarkdown) ## ## ─ Packages ─────────────────────────────────────────────────────────────────── @@ -422,7 +422,7 @@

Session info## genefilter 1.88.0 2024-10-29 [1] Bioconductor 3.20 (R 4.4.2) ## generics 0.1.3 2022-07-05 [1] RSPM (R 4.4.0) ## GenomeInfoDb * 1.42.1 2024-11-28 [1] Bioconductor 3.20 (R 4.4.2) -## GenomeInfoDbData 1.2.13 2024-12-04 [1] Bioconductor +## GenomeInfoDbData 1.2.13 2024-12-05 [1] Bioconductor ## GenomicRanges * 1.58.0 2024-10-29 [1] Bioconductor 3.20 (R 4.4.2) ## getopt 1.20.4 2023-10-01 [1] RSPM (R 4.4.0) ## ggbeeswarm 0.7.2 2023-04-29 [1] RSPM (R 4.4.0) @@ -504,7 +504,7 @@

Session info## mice 3.17.0 2024-11-27 [1] RSPM (R 4.4.0) ## microbiome 1.28.0 2024-10-29 [1] Bioconductor 3.20 (R 4.4.2) ## MicrobiomeBenchmarkData * 1.8.0 2024-10-31 [1] Bioconductor 3.20 (R 4.4.2) -## MicrobiomeBenchmarkDataAnalyses * 0.99.11 2024-12-04 [1] local +## MicrobiomeBenchmarkDataAnalyses * 0.99.12 2024-12-05 [1] local ## MicrobiomeStat 1.2 2024-04-01 [1] RSPM (R 4.4.0) ## mime 0.12 2021-09-28 [1] RSPM (R 4.4.0) ## miniUI 0.1.1.1 2018-05-18 [1] RSPM (R 4.4.0) @@ -658,7 +658,7 @@

Session info## yulab.utils 0.1.8 2024-11-07 [1] RSPM (R 4.4.0) ## zCompositions 1.5.0-4 2024-06-19 [1] RSPM (R 4.4.0) ## zinbwave 1.28.0 2024-10-29 [1] Bioconductor 3.20 (R 4.4.2) -## ZINQ 2.0 2024-12-04 [1] Github (wdl2459/ZINQ-v2@40391a6) +## ZINQ 2.0 2024-12-05 [1] Github (wdl2459/ZINQ-v2@40391a6) ## zlibbioc 1.52.0 2024-10-29 [1] Bioconductor 3.20 (R 4.4.2) ## zoo 1.8-12 2023-04-13 [1] RSPM (R 4.4.0) ## diff --git a/articles/HMP_2012_WMS_gingival.html b/articles/HMP_2012_WMS_gingival.html index d3b24a7..5785a1f 100644 --- a/articles/HMP_2012_WMS_gingival.html +++ b/articles/HMP_2012_WMS_gingival.html @@ -32,7 +32,7 @@ MicrobiomeBenchmarkDataAnalyses - 0.99.11 + 0.99.12

@@ -229,14 +229,14 @@

Differential abundance analysis DA_output <- purrr::list_flatten(DA_output, name_spec = "{inner}") DA_output <- purrr::discard(DA_output, is.null) }) -
## Running method 1: DA_DESeq2.1 - 2024-12-04 23:53:06.44456
-
## Running method 2: DA_DESeq2.1 - 2024-12-04 23:53:10.536615
-
## Running method 3: DA_limma.1 - 2024-12-04 23:53:15.657624
-
## Running method 4: DA_limma.1 - 2024-12-04 23:53:15.68115
-
## Running method 5: DA_metagenomeSeq.1 - 2024-12-04 23:53:15.697864
-
## Running method 6: DA_ALDEx2.1 - 2024-12-04 23:53:16.169794
-
## Running method 7: DA_MAST.1 - 2024-12-04 23:53:17.964839
-
## Running method 8: DA_Seurat.1 - 2024-12-04 23:53:19.185622
+
## Running method 1: DA_DESeq2.1 - 2024-12-05 05:53:37.353985
+
## Running method 2: DA_DESeq2.1 - 2024-12-05 05:53:41.482595
+
## Running method 3: DA_limma.1 - 2024-12-05 05:53:46.682774
+
## Running method 4: DA_limma.1 - 2024-12-05 05:53:46.706542
+
## Running method 5: DA_metagenomeSeq.1 - 2024-12-05 05:53:46.723061
+
## Running method 6: DA_ALDEx2.1 - 2024-12-05 05:53:47.202794
+
## Running method 7: DA_MAST.1 - 2024-12-05 05:53:49.012416
+
## Running method 8: DA_Seurat.1 - 2024-12-05 05:53:50.24576
## For a (much!) faster implementation of the Wilcoxon Rank Sum Test,
 ## (default method for FindMarkers) please install the presto package
 ## --------------------------------------------
@@ -246,23 +246,23 @@ 
Differential abundance analysis## After installation of presto, Seurat will automatically use the more 
 ## efficient implementation (no further action necessary).
 ## This message will be shown once per session
-
## Running method 9: ancombc.1 - 2024-12-04 23:53:19.740719
-
## Running method 10: wilcox.3 - 2024-12-04 23:53:19.789119
-
## Running method 11: wilcox.4 - 2024-12-04 23:53:19.995617
-
## Running method 12: ZINQ.9 - 2024-12-04 23:53:20.125108
-
## Running method 13: ZINQ.10 - 2024-12-04 23:53:21.568033
-
## Running method 14: lefse.12 - 2024-12-04 23:53:22.718059
+
## Running method 9: ancombc.1 - 2024-12-05 05:53:50.791175
+
## Running method 10: wilcox.3 - 2024-12-05 05:53:50.839201
+
## Running method 11: wilcox.4 - 2024-12-05 05:53:51.048368
+
## Running method 12: ZINQ.9 - 2024-12-05 05:53:51.178807
+
## Running method 13: ZINQ.10 - 2024-12-05 05:53:52.633139
+
## Running method 14: lefse.12 - 2024-12-05 05:53:53.787877
## Running lefse original
## The outcome variable is specified as 'body_subsite' and the reference category is 'subgingival_plaque'.
 ##  See `?factor` or `?relevel` to change the reference category.
-
## Running method 15: lefse.13 - 2024-12-04 23:53:23.143877
+
## Running method 15: lefse.13 - 2024-12-05 05:53:54.218306
## Running lefse original
## The outcome variable is specified as 'body_subsite' and the reference category is 'subgingival_plaque'.
 ##  See `?factor` or `?relevel` to change the reference category.
 tim
##    user  system elapsed 
-##  16.917   0.092  16.995
+## 17.082 0.100 17.154
@@ -363,7 +363,7 @@

Session Info## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz Etc/UTC -## date 2024-12-04 +## date 2024-12-05 ## pandoc 3.5 @ /usr/bin/ (via rmarkdown) ## ## ─ Packages ─────────────────────────────────────────────────────────────────── @@ -462,7 +462,7 @@

Session Info## genefilter 1.88.0 2024-10-29 [1] Bioconductor 3.20 (R 4.4.2) ## generics 0.1.3 2022-07-05 [1] RSPM (R 4.4.0) ## GenomeInfoDb * 1.42.1 2024-11-28 [1] Bioconductor 3.20 (R 4.4.2) -## GenomeInfoDbData 1.2.13 2024-12-04 [1] Bioconductor +## GenomeInfoDbData 1.2.13 2024-12-05 [1] Bioconductor ## GenomicRanges * 1.58.0 2024-10-29 [1] Bioconductor 3.20 (R 4.4.2) ## getopt 1.20.4 2023-10-01 [1] RSPM (R 4.4.0) ## ggbeeswarm 0.7.2 2023-04-29 [1] RSPM (R 4.4.0) @@ -544,7 +544,7 @@

Session Info## mice 3.17.0 2024-11-27 [1] RSPM (R 4.4.0) ## microbiome 1.28.0 2024-10-29 [1] Bioconductor 3.20 (R 4.4.2) ## MicrobiomeBenchmarkData * 1.8.0 2024-10-31 [1] Bioconductor 3.20 (R 4.4.2) -## MicrobiomeBenchmarkDataAnalyses * 0.99.11 2024-12-04 [1] local +## MicrobiomeBenchmarkDataAnalyses * 0.99.12 2024-12-05 [1] local ## MicrobiomeStat 1.2 2024-04-01 [1] RSPM (R 4.4.0) ## mime 0.12 2021-09-28 [1] RSPM (R 4.4.0) ## miniUI 0.1.1.1 2018-05-18 [1] RSPM (R 4.4.0) @@ -698,7 +698,7 @@

Session Info## yulab.utils 0.1.8 2024-11-07 [1] RSPM (R 4.4.0) ## zCompositions 1.5.0-4 2024-06-19 [1] RSPM (R 4.4.0) ## zinbwave 1.28.0 2024-10-29 [1] Bioconductor 3.20 (R 4.4.2) -## ZINQ 2.0 2024-12-04 [1] Github (wdl2459/ZINQ-v2@40391a6) +## ZINQ 2.0 2024-12-05 [1] Github (wdl2459/ZINQ-v2@40391a6) ## zlibbioc 1.52.0 2024-10-29 [1] Bioconductor 3.20 (R 4.4.2) ## zoo 1.8-12 2023-04-13 [1] RSPM (R 4.4.0) ## diff --git a/articles/MicrobiomeBenchmarkDataAnalyses.html b/articles/MicrobiomeBenchmarkDataAnalyses.html index 7c48e34..192f62f 100644 --- a/articles/MicrobiomeBenchmarkDataAnalyses.html +++ b/articles/MicrobiomeBenchmarkDataAnalyses.html @@ -32,7 +32,7 @@ MicrobiomeBenchmarkDataAnalyses - 0.99.11 + 0.99.12

diff --git a/articles/Ravel_2011_16S_BV.html b/articles/Ravel_2011_16S_BV.html index ef48e89..417e244 100644 --- a/articles/Ravel_2011_16S_BV.html +++ b/articles/Ravel_2011_16S_BV.html @@ -32,7 +32,7 @@ MicrobiomeBenchmarkDataAnalyses - 0.99.11 + 0.99.12 @@ -296,7 +296,7 @@

Run DA methods}) tim 
##    user  system elapsed 
-##   8.849   0.127   8.993
+## 8.866 0.128 9.010
@@ -1469,7 +1469,7 @@

Session info## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz Etc/UTC -## date 2024-12-04 +## date 2024-12-05 ## pandoc 3.5 @ /usr/bin/ (via rmarkdown) ## ## ─ Packages ─────────────────────────────────────────────────────────────────── @@ -1573,7 +1573,7 @@

Session info## genefilter 1.88.0 2024-10-29 [1] Bioconductor 3.20 (R 4.4.2) ## generics 0.1.3 2022-07-05 [1] RSPM (R 4.4.0) ## GenomeInfoDb * 1.42.1 2024-11-28 [1] Bioconductor 3.20 (R 4.4.2) -## GenomeInfoDbData 1.2.13 2024-12-04 [1] Bioconductor +## GenomeInfoDbData 1.2.13 2024-12-05 [1] Bioconductor ## GenomicRanges * 1.58.0 2024-10-29 [1] Bioconductor 3.20 (R 4.4.2) ## getopt 1.20.4 2023-10-01 [1] RSPM (R 4.4.0) ## ggbeeswarm 0.7.2 2023-04-29 [1] RSPM (R 4.4.0) @@ -1657,7 +1657,7 @@

Session info## mice 3.17.0 2024-11-27 [1] RSPM (R 4.4.0) ## microbiome 1.28.0 2024-10-29 [1] Bioconductor 3.20 (R 4.4.2) ## MicrobiomeBenchmarkData * 1.8.0 2024-10-31 [1] Bioconductor 3.20 (R 4.4.2) -## MicrobiomeBenchmarkDataAnalyses * 0.99.11 2024-12-04 [1] local +## MicrobiomeBenchmarkDataAnalyses * 0.99.12 2024-12-05 [1] local ## MicrobiomeStat 1.2 2024-04-01 [1] RSPM (R 4.4.0) ## mime 0.12 2021-09-28 [1] RSPM (R 4.4.0) ## miniUI 0.1.1.1 2018-05-18 [1] RSPM (R 4.4.0) @@ -1814,7 +1814,7 @@

Session info## yulab.utils 0.1.8 2024-11-07 [1] RSPM (R 4.4.0) ## zCompositions 1.5.0-4 2024-06-19 [1] RSPM (R 4.4.0) ## zinbwave 1.28.0 2024-10-29 [1] Bioconductor 3.20 (R 4.4.2) -## ZINQ 2.0 2024-12-04 [1] Github (wdl2459/ZINQ-v2@40391a6) +## ZINQ 2.0 2024-12-05 [1] Github (wdl2459/ZINQ-v2@40391a6) ## zlibbioc 1.52.0 2024-10-29 [1] Bioconductor 3.20 (R 4.4.2) ## zoo 1.8-12 2023-04-13 [1] RSPM (R 4.4.0) ## diff --git a/articles/Stammler_2016_16S_spikein.html b/articles/Stammler_2016_16S_spikein.html index 375438a..ea8ad3a 100644 --- a/articles/Stammler_2016_16S_spikein.html +++ b/articles/Stammler_2016_16S_spikein.html @@ -32,7 +32,7 @@ MicrobiomeBenchmarkDataAnalyses - 0.99.11 + 0.99.12

@@ -167,12 +167,12 @@

Tranform with TSS (relativ 

 tss_fun <- function(x) (x + 1) / sum((x + 1))
+# tss_fun <- function(x) (x + 1) / sum((x + 1))
 # tss_fun <- function(x) log((x + 1) / sum((x + 1)))
-# tss_fun <- function(x) (x) / sum((x))
 gmn_fun <- function(x) (x + 1) / exp(mean(log((x + 1))))
 # gnm_fun <- function(x) (x + 1) / prod((x + 1)^(1 / length(x)))
 # gmn_fun <- function(x) log((x + 1) / exp(mean(log((x + 1)))))
-assay(tse, "TSS") <- apply(assay(tse, 'counts'), 2,  tss_fun)
+assay(tse, "TSS") <- apply(assay(tse, 'counts'), 2, tss_fun)
 assay(tse, "GMN") <- apply(assay(tse, 'counts'), 2, gmn_fun)
@@ -326,7 +326,7 @@

Ranking bind_rows(.id = "feature") }) #> user system elapsed -#> 82.728 0.080 82.823 +#> 82.070 0.113 82.187

Get coefficient of variation for all features:

 gmn_mat <- assay(tse, "GMN")
@@ -336,7 +336,7 @@ 
Ranking        bind_rows(.id = "feature")
 })
 #>    user  system elapsed 
-#>  82.329   0.004  82.335
+#> 82.071 0.008 82.081

Add rankings

 tss <- tss_cv |> 
@@ -348,6 +348,7 @@ 
Ranking        ranking = min_rank(cv)
     )
 
+
 tss$mean <- apply(tss_mat, 1, mean)
 gmn$mean <- apply(gmn_mat, 1, mean)
 
@@ -381,10 +382,10 @@ 
Ranking        spikein = factor(spikein, levels = c("Spike-in", "Non-spike-in"))
     ) |> 
     ggplot(aes(x = tss_ranking, y = gmn_ranking)) +
-    geom_abline(slope = 1, intercept = 0, linetype = 2, linewidth = 0.3) +
     geom_point(
         aes(color = spikein, shape = spikein, size = spikein)
     ) +
+    geom_abline(slope = 1, intercept = 0, linetype = 2, linewidth = 0.3) +
     geom_label_repel(
         data = filter(dat, feature_label != ""),
         mapping = aes(label = feature_label), 
@@ -392,6 +393,8 @@ 
Ranking    )+
     scale_fill_viridis_c(option = "C") +
     scale_size_manual(values = c(3, 1)) +
+    scale_color_manual(values = c("gray20", "gray70")) +
+    scale_shape_manual(values = c(20, 4)) +
     scale_x_continuous(labels = \(x) format(x, big.mark = ",")) +
     scale_y_continuous(labels = \(x) format(x, big.mark = ",")) +
     labs(
@@ -406,9 +409,9 @@ 
Rankingp_b <- dat |> 
     ggplot(aes(x = tss_ranking, y = gmn_ranking)) +
     geom_hex(
-        color = "white"
+        color = "black", alpha = 0.9
     ) +
-    geom_abline(slope = 1, intercept = 0, linetype = 2, linewidth = 0.3) +
+    geom_abline(slope = 1, intercept = 0, linetype = 2, linewidth = 0.3, color = "red") +
     # geom_label_repel(
     #     data = filter(dat, feature_label != ""),
     #     mapping = aes(label = feature_label),
@@ -432,16 +435,17 @@ 
Ranking    plotlist = list(p_a, p_b), 
     labels = c("A", "B"),
     nrow = 1
-)
-plts_1
-

+) 
+plts_1
+

+
 hexFun <- function(myDat, xvar, yvar) {
     xvar <- enquo(xvar)
     yvar <- enquo(yvar)
     myDat |> 
         ggplot(aes(!!xvar, !!yvar)) +
-        geom_hex(color = "white") +
+        geom_hex(color = "black", alpha = 0.9) +
         geom_label_repel(
             data = filter(myDat, feature_label != ""),
             mapping = aes(label = feature_label),
@@ -487,7 +491,7 @@ 
Ranking    ncol = 2, nrow = 2
 )
 plts
-

+

@@ -499,7 +503,7 @@

Conclusion

Session info

-
+
 sessioninfo::session_info()
 #> ─ Session info ───────────────────────────────────────────────────────────────
 #>  setting  value
@@ -511,7 +515,7 @@ 
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@@ -587,7 +591,7 @@ 
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diff --git a/articles/Stammler_2016_16S_spikein_files/figure-html/unnamed-chunk-15-1.png b/articles/Stammler_2016_16S_spikein_files/figure-html/unnamed-chunk-15-1.png
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@@ -17,7 +17,7 @@
       
       
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         MicrobiomeBenchmarkDataAnalyses
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Citation

Gamboa-Tuz S (2024). MicrobiomeBenchmarkDataAnalyses: Benchmarking analyses with the MicrobiomeBenchmarkData package. -R package version 0.99.11, https://github.com/waldronlab/MicrobiomeBenchmarkDataAnalyses. +R package version 0.99.12, https://github.com/waldronlab/MicrobiomeBenchmarkDataAnalyses. 

@Manual{,
   title = {MicrobiomeBenchmarkDataAnalyses: Benchmarking analyses with the MicrobiomeBenchmarkData package},
   author = {Samuel David Gamboa-Tuz},
   year = {2024},
-  note = {R package version 0.99.11},
+  note = {R package version 0.99.12},
   url = {https://github.com/waldronlab/MicrobiomeBenchmarkDataAnalyses},
 }
diff --git a/index.html b/index.html index f09bef1..c1ce858 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ MicrobiomeBenchmarkDataAnalyses - 0.99.11 + 0.99.12

diff --git a/pkgdown.yml b/pkgdown.yml index 945435b..9e7c377 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -9,7 +9,7 @@ articles: MicrobiomeBenchmarkDataAnalyses: MicrobiomeBenchmarkDataAnalyses.html articles/Ravel_2011_16S_BV: Ravel_2011_16S_BV.html articles/Stammler_2016_16S_spikein: Stammler_2016_16S_spikein.html -last_built: 2024-12-04T23:43Z +last_built: 2024-12-05T05:43Z urls: reference: http://waldronlab.io/MicrobiomeBenchmarkDataAnalyses/reference article: http://waldronlab.io/MicrobiomeBenchmarkDataAnalyses/articles diff --git a/reference/DA_ZINQ.html b/reference/DA_ZINQ.html index 91e7475..9cac41c 100644 --- a/reference/DA_ZINQ.html +++ b/reference/DA_ZINQ.html @@ -18,7 +18,7 @@ MicrobiomeBenchmarkDataAnalyses - 0.99.11 + 0.99.12 diff --git a/reference/DA_ancombc.html b/reference/DA_ancombc.html index ac8e8ab..2489cfe 100644 --- a/reference/DA_ancombc.html +++ b/reference/DA_ancombc.html @@ -18,7 +18,7 @@ MicrobiomeBenchmarkDataAnalyses - 0.99.11 + 0.99.12 diff --git a/reference/DA_lefse.html b/reference/DA_lefse.html index 6de0916..097370a 100644 --- a/reference/DA_lefse.html +++ b/reference/DA_lefse.html @@ -18,7 +18,7 @@ MicrobiomeBenchmarkDataAnalyses - 0.99.11 + 0.99.12 diff --git a/reference/DA_wilcox.html b/reference/DA_wilcox.html index 5008c7f..ce20b53 100644 --- a/reference/DA_wilcox.html +++ b/reference/DA_wilcox.html @@ -17,7 +17,7 @@ MicrobiomeBenchmarkDataAnalyses - 0.99.11 + 0.99.12 diff --git a/reference/MicrobiomeBenchmarkDataAnalyses.html b/reference/MicrobiomeBenchmarkDataAnalyses.html index 66410b2..83a6a97 100644 --- a/reference/MicrobiomeBenchmarkDataAnalyses.html +++ b/reference/MicrobiomeBenchmarkDataAnalyses.html @@ -18,7 +18,7 @@ MicrobiomeBenchmarkDataAnalyses - 0.99.11 + 0.99.12 diff --git a/reference/editMiaTaxaNames.html b/reference/editMiaTaxaNames.html index d853542..241b7a8 100644 --- a/reference/editMiaTaxaNames.html +++ b/reference/editMiaTaxaNames.html @@ -19,7 +19,7 @@ MicrobiomeBenchmarkDataAnalyses - 0.99.11 + 0.99.12 diff --git a/reference/filterTaxa.html b/reference/filterTaxa.html index 4db4deb..efb4d2a 100644 --- a/reference/filterTaxa.html +++ b/reference/filterTaxa.html @@ -19,7 +19,7 @@ MicrobiomeBenchmarkDataAnalyses - 0.99.11 + 0.99.12 diff --git a/reference/get_direction_cols.html b/reference/get_direction_cols.html index d8064e2..c1da7b9 100644 --- a/reference/get_direction_cols.html +++ b/reference/get_direction_cols.html @@ -19,7 +19,7 @@ MicrobiomeBenchmarkDataAnalyses - 0.99.11 + 0.99.12 diff --git a/reference/get_meth_class.html b/reference/get_meth_class.html index 436d424..8755e89 100644 --- a/reference/get_meth_class.html +++ b/reference/get_meth_class.html @@ -18,7 +18,7 @@ MicrobiomeBenchmarkDataAnalyses - 0.99.11 + 0.99.12 diff --git a/reference/index.html b/reference/index.html index 1d25c79..cd226a8 100644 --- a/reference/index.html +++ b/reference/index.html @@ -17,7 +17,7 @@ MicrobiomeBenchmarkDataAnalyses - 0.99.11 + 0.99.12 diff --git a/reference/lefser2.html b/reference/lefser2.html index 3532fb0..fc8f5a1 100644 --- a/reference/lefser2.html +++ b/reference/lefser2.html @@ -19,7 +19,7 @@ MicrobiomeBenchmarkDataAnalyses - 0.99.11 + 0.99.12 diff --git a/reference/log2_fold_change.html b/reference/log2_fold_change.html index f351d23..e9ef437 100644 --- a/reference/log2_fold_change.html +++ b/reference/log2_fold_change.html @@ -18,7 +18,7 @@ MicrobiomeBenchmarkDataAnalyses - 0.99.11 + 0.99.12 diff --git a/reference/norm_clr.html b/reference/norm_clr.html index aae53cb..744b209 100644 --- a/reference/norm_clr.html +++ b/reference/norm_clr.html @@ -19,7 +19,7 @@ MicrobiomeBenchmarkDataAnalyses - 0.99.11 + 0.99.12 diff --git a/reference/norm_tss.html b/reference/norm_tss.html index 67fe65a..f715b9c 100644 --- a/reference/norm_tss.html +++ b/reference/norm_tss.html @@ -17,7 +17,7 @@ MicrobiomeBenchmarkDataAnalyses - 0.99.11 + 0.99.12 diff --git a/reference/plot_enrichment.html b/reference/plot_enrichment.html index d382c5a..4add296 100644 --- a/reference/plot_enrichment.html +++ b/reference/plot_enrichment.html @@ -17,7 +17,7 @@ MicrobiomeBenchmarkDataAnalyses - 0.99.11 + 0.99.12 diff --git a/reference/plot_enrichment_2.html b/reference/plot_enrichment_2.html index 4da41ab..346921f 100644 --- a/reference/plot_enrichment_2.html +++ b/reference/plot_enrichment_2.html @@ -17,7 +17,7 @@ MicrobiomeBenchmarkDataAnalyses - 0.99.11 + 0.99.12 diff --git a/reference/plot_positives.html b/reference/plot_positives.html index f299ca4..fe1d72d 100644 --- a/reference/plot_positives.html +++ b/reference/plot_positives.html @@ -17,7 +17,7 @@ MicrobiomeBenchmarkDataAnalyses - 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