# Load data from miaTime package library("miaTime") data(SilvermanAGutData, package="miaTime") @@ -321,7 +328,7 @@argument selects the feature to show. Since plotting a lot of features is not advised a maximum of 20 features can plotted at the same time. -Plotting of serial datay
+plotSeries(tse, x = "DAY_ORDER", y = taxa, @@ -330,14 +337,14 @@andPlotting of serial datamean
sdand plotted as a range. Data from different assays can be used for plotting via theassay.type. -+plotSeries(tse[taxa,], x = "DAY_ORDER", colour_by = "Family", linetype_by = "Phylum", assay.type = "relabundance")Additional variables can be used to modify line type aesthetics.
-+plotSeries(tse, x = "DAY_ORDER", y = getTopTaxa(tse, 5), @@ -351,12 +358,12 @@Plotting factor data
+-data(GlobalPatterns, package="mia") se <- GlobalPatterns plotColTile(se,"SampleType","Primer") + theme(axis.text.x.top = element_text(angle = 45, hjust = 0))+
DMN fit plotting @@ -368,7 +375,7 @@
DMN fit plottinggetDMN and
getBestDMNFit). To visualize the fit using e.g. “laplace” as a measure of goodness of fit: -+-data(dmn_se, package = "mia") names(metadata(dmn_se)) #> [1] "DMN" @@ -377,18 +384,11 @@DMN fit plotting#> Warning: 'getDMN' is deprecated. #> Use 'cluster' instead. #> See help("Deprecated") and help("Now runDMN and calculateDMN are deprecated. Use cluster with DMMParam parameter and full parameter set as true instead.-deprecated").
+
Serial data ordination and trajectories
--if(!requireNamespace("devtools", quietly = TRUE)){ - BiocManager::install("devtools") -} -if(!requireNamespace("miaTime", quietly = TRUE)){ - devtools::install_github("microbiome/miaTime", upgrade = "never") -}Principal Coordinates Analysis using Bray-Curtis dissimilarity on the
hitchip1006dataset:diff --git a/articles/miaViz_files/figure-html/unnamed-chunk-15-1.png b/articles/miaViz_files/figure-html/unnamed-chunk-15-1.png index f3c24a31..c96b861e 100644 Binary files a/articles/miaViz_files/figure-html/unnamed-chunk-15-1.png and b/articles/miaViz_files/figure-html/unnamed-chunk-15-1.png differ diff --git a/articles/miaViz_files/figure-html/unnamed-chunk-17-1.png b/articles/miaViz_files/figure-html/unnamed-chunk-17-1.png index 17c8c24e..44d89dbb 100644 Binary files a/articles/miaViz_files/figure-html/unnamed-chunk-17-1.png and b/articles/miaViz_files/figure-html/unnamed-chunk-17-1.png differ diff --git a/articles/miaViz_files/figure-html/unnamed-chunk-22-1.png b/articles/miaViz_files/figure-html/unnamed-chunk-22-1.png deleted file mode 100644 index c750ea3f..00000000 Binary files a/articles/miaViz_files/figure-html/unnamed-chunk-22-1.png and /dev/null differ diff --git a/articles/miaViz_files/figure-html/unnamed-chunk-23-1.png b/articles/miaViz_files/figure-html/unnamed-chunk-23-1.png index c5859f14..c750ea3f 100644 Binary files a/articles/miaViz_files/figure-html/unnamed-chunk-23-1.png and b/articles/miaViz_files/figure-html/unnamed-chunk-23-1.png differ diff --git a/articles/miaViz_files/figure-html/unnamed-chunk-24-1.png b/articles/miaViz_files/figure-html/unnamed-chunk-24-1.png new file mode 100644 index 00000000..c5859f14 Binary files /dev/null and b/articles/miaViz_files/figure-html/unnamed-chunk-24-1.png differ diff --git a/pkgdown.yml b/pkgdown.yml index 511c74a8..ea478840 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,5 +3,5 @@ pkgdown: 2.0.7 pkgdown_sha: ~ articles: miaViz: miaViz.html -last_built: 2023-10-05T07:56Z +last_built: 2023-10-05T08:26Z diff --git a/reference/Rplot008.png b/reference/Rplot008.png index 4480afe6..7dee2bc3 100644 Binary files a/reference/Rplot008.png and b/reference/Rplot008.png differ diff --git a/reference/plotAbundanceDensity-1.png b/reference/plotAbundanceDensity-1.png index 1e47cb53..ce088fd0 100644 Binary files a/reference/plotAbundanceDensity-1.png and b/reference/plotAbundanceDensity-1.png differ diff --git a/reference/plotAbundanceDensity-2.png b/reference/plotAbundanceDensity-2.png index 2d862355..29b9e703 100644 Binary files a/reference/plotAbundanceDensity-2.png and b/reference/plotAbundanceDensity-2.png differ diff --git a/reference/plotAbundanceDensity-6.png b/reference/plotAbundanceDensity-6.png index 1bd70366..6839ceb6 100644 Binary files a/reference/plotAbundanceDensity-6.png and b/reference/plotAbundanceDensity-6.png differ diff --git a/reference/plotAbundanceDensity-7.png b/reference/plotAbundanceDensity-7.png index 9d9ca14c..465425d2 100644 Binary files a/reference/plotAbundanceDensity-7.png and b/reference/plotAbundanceDensity-7.png differ diff --git a/reference/plotCCA-1.png b/reference/plotCCA-1.png index 115e69a2..08c344b2 100644 Binary files a/reference/plotCCA-1.png and b/reference/plotCCA-1.png differ diff --git a/reference/plotCCA-2.png b/reference/plotCCA-2.png index 3c4e3113..9910ecbc 100644 Binary files a/reference/plotCCA-2.png and b/reference/plotCCA-2.png differ diff --git a/reference/plotCCA-3.png b/reference/plotCCA-3.png index 4f2b5509..21c5403b 100644 Binary files a/reference/plotCCA-3.png and b/reference/plotCCA-3.png differ diff --git a/reference/plotCCA-4.png b/reference/plotCCA-4.png index b163576e..e9dc4ad5 100644 Binary files a/reference/plotCCA-4.png and b/reference/plotCCA-4.png differ diff --git a/reference/plotCCA-5.png b/reference/plotCCA-5.png index b31a7873..36d435c5 100644 Binary files a/reference/plotCCA-5.png and b/reference/plotCCA-5.png differ diff --git a/reference/plotCCA-6.png b/reference/plotCCA-6.png index cdd2bfe8..c2676416 100644 Binary files a/reference/plotCCA-6.png and b/reference/plotCCA-6.png differ diff --git a/reference/plotDMN-1.png b/reference/plotDMN-1.png index 0b4a6a78..b14b7d35 100644 Binary files a/reference/plotDMN-1.png and b/reference/plotDMN-1.png differ diff --git a/reference/plotGraph-1.png b/reference/plotGraph-1.png index 879f4ac0..919502e1 100644 Binary files a/reference/plotGraph-1.png and b/reference/plotGraph-1.png differ diff --git a/reference/plotGraph-6.png b/reference/plotGraph-6.png index 55a7a911..69aaf7c4 100644 Binary files a/reference/plotGraph-6.png and b/reference/plotGraph-6.png differ diff --git a/reference/plotGraph-7.png b/reference/plotGraph-7.png index af1b3dfc..4a7a34d0 100644 Binary files a/reference/plotGraph-7.png and b/reference/plotGraph-7.png differ diff --git a/reference/plotGraph-8.png b/reference/plotGraph-8.png index 9dd989f1..1b895431 100644 Binary files a/reference/plotGraph-8.png and b/reference/plotGraph-8.png differ diff --git a/reference/treeData.html b/reference/treeData.html index 1813e8b8..fc3d6d84 100644 --- a/reference/treeData.html +++ b/reference/treeData.html @@ -183,18 +183,18 @@Examples
#> #> # The associated data tibble abstraction: 38,431 × 4 #> # The 'node', 'label' and 'isTip' are from the phylo tree. -#> node label isTip test -#> <int> <chr> <lgl> <dbl> -#> 1 1 549322 TRUE 1.04 -#> 2 2 522457 TRUE -0.567 -#> 3 3 951 TRUE -0.213 -#> 4 4 244423 TRUE -1.07 -#> 5 5 586076 TRUE 0.577 -#> 6 6 246140 TRUE -2.08 -#> 7 7 143239 TRUE 0.702 -#> 8 8 244960 TRUE 2.19 -#> 9 9 255340 TRUE 0.650 -#> 10 10 144887 TRUE -0.726 +#> node label isTip test +#> <int> <chr> <lgl> <dbl> +#> 1 1 549322 TRUE -1.61 +#> 2 2 522457 TRUE 1.10 +#> 3 3 951 TRUE -0.141 +#> 4 4 244423 TRUE 0.189 +#> 5 5 586076 TRUE -0.519 +#> 6 6 246140 TRUE -0.0117 +#> 7 7 143239 TRUE 0.544 +#> 8 8 244960 TRUE 0.838 +#> 9 9 255340 TRUE -0.532 +#> 10 10 144887 TRUE 1.57 #> # ℹ 38,421 more rows
