diff --git a/404.html b/404.html index 42d927d..8074ca0 100644 --- a/404.html +++ b/404.html @@ -6,7 +6,7 @@ Page not found (404) • ampvis2 - + @@ -40,7 +40,7 @@ ampvis2 - 2.8.7 + 2.8.8 @@ -108,7 +108,7 @@

Page not found (404)

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Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/ISSUE_TEMPLATE.html b/ISSUE_TEMPLATE.html index d532984..77bcba0 100644 --- a/ISSUE_TEMPLATE.html +++ b/ISSUE_TEMPLATE.html @@ -1,5 +1,5 @@ -NA • ampvis2NA • ampvis2License • ampvis2 + @@ -41,7 +41,7 @@ ampvis2 - 2.8.7 + 2.8.8 @@ -402,7 +402,7 @@

Read more

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Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/articles/ampvis2_files/figure-html/unnamed-chunk-10-1.png b/articles/ampvis2_files/figure-html/unnamed-chunk-10-1.png index 1a7670b..af0e1fa 100644 Binary files a/articles/ampvis2_files/figure-html/unnamed-chunk-10-1.png and b/articles/ampvis2_files/figure-html/unnamed-chunk-10-1.png differ diff --git a/articles/ampvis2_files/figure-html/unnamed-chunk-12-1.png b/articles/ampvis2_files/figure-html/unnamed-chunk-12-1.png index b06f1bc..0ffda8a 100644 Binary files a/articles/ampvis2_files/figure-html/unnamed-chunk-12-1.png and b/articles/ampvis2_files/figure-html/unnamed-chunk-12-1.png differ diff --git a/articles/ampvis2_files/figure-html/unnamed-chunk-13-1.png b/articles/ampvis2_files/figure-html/unnamed-chunk-13-1.png index 62a29fd..2360bb3 100644 Binary files a/articles/ampvis2_files/figure-html/unnamed-chunk-13-1.png and b/articles/ampvis2_files/figure-html/unnamed-chunk-13-1.png differ diff --git a/articles/ampvis2_files/figure-html/unnamed-chunk-14-1.png b/articles/ampvis2_files/figure-html/unnamed-chunk-14-1.png index 874341b..6911943 100644 Binary files a/articles/ampvis2_files/figure-html/unnamed-chunk-14-1.png and b/articles/ampvis2_files/figure-html/unnamed-chunk-14-1.png differ diff --git a/articles/ampvis2_files/figure-html/unnamed-chunk-15-1.png b/articles/ampvis2_files/figure-html/unnamed-chunk-15-1.png index fcdd7eb..e276951 100644 Binary files a/articles/ampvis2_files/figure-html/unnamed-chunk-15-1.png and b/articles/ampvis2_files/figure-html/unnamed-chunk-15-1.png differ diff --git a/articles/ampvis2_files/figure-html/unnamed-chunk-9-1.png b/articles/ampvis2_files/figure-html/unnamed-chunk-9-1.png index 2c7e250..4078bcb 100644 Binary files a/articles/ampvis2_files/figure-html/unnamed-chunk-9-1.png and b/articles/ampvis2_files/figure-html/unnamed-chunk-9-1.png differ diff --git a/articles/faq.html b/articles/faq.html index 9ffbad3..c5eca17 100644 --- a/articles/faq.html +++ b/articles/faq.html @@ -6,7 +6,7 @@ Frequently Asked Questions • ampvis2 - + @@ -41,7 +41,7 @@ ampvis2 - 2.8.7 + 2.8.8 @@ -173,7 +173,7 @@

Custom distance matrix for

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Site built with pkgdown 2.0.7.

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Site built with pkgdown 2.0.9.

diff --git a/articles/index.html b/articles/index.html index f18b249..9bcf27d 100644 --- a/articles/index.html +++ b/articles/index.html @@ -1,5 +1,5 @@ -Articles • ampvis2Articles • ampvis2Authors and Citation • ampvis2 + @@ -41,7 +41,7 @@ ampvis2 - 2.8.7 + 2.8.8 @@ -109,11 +109,11 @@

Get startedRStudio Docker container

A Docker container based on the rocker/rstudio image is also provided with ampvis2 preinstalled. This is ideal for complete reproducibility and portability. All you need to do is install Docker and then run:

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docker run -d \
-  -e "PASSWORD=supersafepassword" \
-  -v "local/folder/to/mount":/home/rstudio \
-  -p 8787:8787 \
-  ghcr.io/kasperskytte/ampvis2:main
+
docker run -d \
+  -e "PASSWORD=supersafepassword" \
+  -v "local/folder/to/mount":/home/rstudio \
+  -p 8787:8787 \
+  ghcr.io/kasperskytte/ampvis2:main

Access RStudio server through a browser at http://localhost:8787 with username rstudio. Ideally use a specific version tag, fx v2.7.31, instead of main to not just pull the latest image every time.

@@ -189,7 +189,7 @@

Dev status

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Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.0.9.

diff --git a/pkgdown.yml b/pkgdown.yml index 31e44e5..9282259 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -1,10 +1,10 @@ -pandoc: 2.19.2 -pkgdown: 2.0.7 +pandoc: 3.1.11 +pkgdown: 2.0.9 pkgdown_sha: ~ articles: ampvis2: ampvis2.html faq: faq.html -last_built: 2024-01-17T10:51Z +last_built: 2024-05-15T11:58Z urls: reference: https://kasperskytte.github.io/ampvis2/reference article: https://kasperskytte.github.io/ampvis2/articles diff --git a/reference/AalborgWWTPs.html b/reference/AalborgWWTPs.html index d9ebecb..4593388 100644 --- a/reference/AalborgWWTPs.html +++ b/reference/AalborgWWTPs.html @@ -1,5 +1,5 @@ -A subset of the MiDAS example data — AalborgWWTPs • ampvis2A subset of the MiDAS example data — AalborgWWTPs • ampvis2MiDAS example data — MiDAS • ampvis2Check whether abundances appear to be read counts (i.e. not normalised) — abundAreCounts • ampvis2Aggregate OTUs to a specific taxonomic level — aggregate_abund • ampvis2Alpha-diversity analysis — amp_alphadiv • ampvis2Boxplot — amp_boxplot • ampvis2Grouped core community analysis — amp_core • ampvis2Export raw DNA sequences — amp_export_fasta • ampvis2Transform ampvis2 objects into a long-format data frame — amp_export_long • ampvis2Export OTU-table — amp_export_otutable • ampvis2Subset ampvis2 objects based on sample metadata — amp_filter_samples • ampvis2Subset ampvis2 objects based on taxonomy — amp_filter_taxa • ampvis2Frequency plot — amp_frequency • ampvis2Heatmap — amp_heatmap • ampvis2(Defunct) Import OTU table from BIOM file — amp_import_biom • ampvis2(Defunct) Import OTU table from USEARCH pipelines — amp_import_usearch • ampvis2(Defunct) Import OTU table from USEARCH pipelines — amp_import_usearch • ampvis2Load data for ampvis2 functions — amp_load • ampvis2Load data for ampvis2 functions — amp_load • ampvis2Merge ampvis2 object(s) — amp_merge_ampvis2 • ampvis2Merge replicate samples — amp_merge_replicates • ampvis2Octave plot — amp_octave • ampvis2Ordination plot — amp_ordinate • ampvis2Network plot — amp_otu_network • ampvis2Rank abundance plot — amp_rankabundance • ampvis2Rarefaction curve — amp_rarecurve • ampvis2Rarefy ampvis2 object — amp_rarefy • ampvis2Tidy up taxonomy — amp_rename • ampvis2Abundance timeseries — amp_timeseries • ampvis2Venn diagram of core OTUs — amp_venn • ampvis2ampvis2 package — ampvis2 • ampvis2Coerce DNAbin object to data.table — as.data.table.DNAbin • ampvis2Check for installed package — checkReqPkg • ampvis2Calculate Jensen-Shannon Divergence distances — dist.JSD • ampvis2Calculate weighted or unweighted UniFrac distances. Adopted from fastUniFrac() from phyloseq — dist.unifrac • ampvis2.onAttach — .onAttach • ampvis2A minimal example of sample metadata — example_metadata • ampvis2A minimal example of an OTU-table — example_otutable • ampvis2A minimal example of taxonomy — example_taxonomy • ampvis2Extract functional information about Genera from the MiDAS field guide — extractFunctions • ampvis2Filter OTUs by a threshold in percent — filter_otus • ampvis2Detect OTU/ASV column in a data frame — findOTUcol • ampvis2Find lowest taxonomic level — getLowestTaxLvl • ampvis2Get data from the MiDAS field guide API — getMiDASFGData • ampvis2Import any file format — import • ampvis2Function reference • ampvis2Check if data has class "ampvis2" — is_ampvis2 • ampvis2Rename OTUs by exact sequence matches from a FASTA file — matchOTUs • ampvis2Functional information about microbes at Genus level — midasfunctions • ampvis2Normalise read counts to 100, i.e. in percent relative abundance per sample — normaliseTo100 • ampvis2Extract/parse taxonomy from a data.frame — parseTaxonomy • ampvis2Pipe operator — %>% • ampvis2Prints ampvis2 object summary (internal function) — print.ampvis2 • ampvis2Prints amp_core plots if margin plots are also generated (internal function) — print.coreplot • ampvis2Print method for figure caption created by amp_ordinate — print.figcaption • ampvis2Prints heatmap+functions plot (internal function) — print.hmfunplot • ampvis2Valid taxonomic levels — tax_levels • ampvis2Unzip file — unzip_file • ampvis2