diff --git a/DESCRIPTION b/DESCRIPTION index 944874e..a0efb27 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: MicrobiomeR Title: Analyze Microbiome Data -Version: 0.4.0 +Version: 0.4.1 Authors@R: c( person("Robert", "Gilmore", email = "rgilmore@umc.edu", role = "cre"), person("Shaurita", "Hutchins", email = "shutchins2@umc.edu", role = "aut")) @@ -15,7 +15,8 @@ Remotes: github::ropensci/taxa, github::grunwaldlab/metacoder, github::joey711/phyloseq, - github::microbiome/microbiome + github::microbiome/microbiome, + github::jonclayden/shades Imports: ape, DT, @@ -50,7 +51,8 @@ Imports: scales, vegan, leaflet, - htmlwidgets + htmlwidgets, + shades Suggests: knitr, testthat, diff --git a/NAMESPACE b/NAMESPACE index c4f8136..75b7976 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -28,6 +28,7 @@ export(is_raw_format) export(metacoder_comp_func_1) export(order_metacoder_data) export(ordination_plot) +export(ordination_plots) export(otu_id_filter) export(otu_prevalence_filter) export(otu_proportion_filter) @@ -155,6 +156,8 @@ importFrom(rlang,enquos) importFrom(rlang,eval_tidy) importFrom(rlang,is_quosure) importFrom(scico,scico) +importFrom(shades,saturation) +importFrom(shades,scalefac) importFrom(stats,median) importFrom(stats,na.omit) importFrom(stats,sd) diff --git a/NEWS.md b/NEWS.md index 4774196..ed8ad51 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +# MicrobiomeR 0.4.1 + +* Fixed wilcoxon pvalue in analysis vignette. +* Updated default color palette for stacked_barplot function. + # MicrobiomeR 0.4.0 ## Renamed functions diff --git a/R/barplot.R b/R/barplot.R index 4585c11..3c26bc0 100644 --- a/R/barplot.R +++ b/R/barplot.R @@ -55,6 +55,7 @@ convert_proportions <- function(melted_df, tax_level) { #' @importFrom ggplot2 ggplot aes annotate geom_bar ylab element_blank element_rect xlab annotate #' @importFrom magrittr %>% #' @importFrom dplyr mutate +#' @importFrom shades scalefac saturation #' @import scales #' @import vegan #' @@ -81,9 +82,15 @@ stacked_barplot <- function(obj, tax_level = "Phylum", fill = "Phylum", xlabel = p <- p + ggplot2::geom_bar(stat = "identity", position = "stack") # Add a palette if default not given. + # Dynamically change palette colors based on number of taxa being input. if (is.null(palette_values)) { - # Dynamically change palette colors based on number of taxa being input. - palette_values <- get_color_palette(pal_func = scico_palette(), color_no = length(unique(mdf[[fill]])), display = FALSE) + pal_func <- combination_palette( + magma = list(palette = viridis::magma, args = list(n=500), range=450:500, rev=TRUE), + inferno = list(palette = viridis::inferno, args = list(n=500), range=100:400, rev=TRUE), + cividis = list(palette = viridis::cividis, args = list(n=500), range=100:200, rev=TRUE), + viridis = list(palette = viridis::viridis, args = list(n=500), range=100:480)) + palette_values <- shades::saturation(get_color_palette(pal_func = pal_func, color_no = length(unique(mdf[[fill]])), display = FALSE), + shades::scalefac(.6)) } # Create the theme diff --git a/R/ordination.R b/R/ordination.R index 2fae021..b9eaef1 100644 --- a/R/ordination.R +++ b/R/ordination.R @@ -87,6 +87,7 @@ ordination_plot <- function(obj, method = "PCoA", distance = "wunifrac", color = #' @return Returns a melted dataframe. #' @family Visualizations #' @rdname ordination_plot +#' @export ordination_plots <- function(obj, methods = c("PCoA", "NMDS"), distances = c("wunifrac", "unifrac", "bray"), color = "TreatmentGroup", select_otu_table = "otu_proportions") { if (is.null(methods)) { diff --git a/docs/CODE_OF_CONDUCT.html b/docs/CODE_OF_CONDUCT.html index 8e5530b..169bd5f 100644 --- a/docs/CODE_OF_CONDUCT.html +++ b/docs/CODE_OF_CONDUCT.html @@ -62,7 +62,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html index deb3d5e..30cd84b 100644 --- a/docs/CONTRIBUTING.html +++ b/docs/CONTRIBUTING.html @@ -62,7 +62,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/ISSUE_TEMPLATE.html b/docs/ISSUE_TEMPLATE.html index a3f66c6..c4ac28c 100644 --- a/docs/ISSUE_TEMPLATE.html +++ b/docs/ISSUE_TEMPLATE.html @@ -62,7 +62,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 9fdeb46..acc2665 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -62,7 +62,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/PULL_REQUEST_TEMPLATE.html b/docs/PULL_REQUEST_TEMPLATE.html index 5ab9bb8..3fba7bb 100644 --- a/docs/PULL_REQUEST_TEMPLATE.html +++ b/docs/PULL_REQUEST_TEMPLATE.html @@ -62,7 +62,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/articles/about.html b/docs/articles/about.html index 64db9f6..4ed5914 100644 --- a/docs/articles/about.html +++ b/docs/articles/about.html @@ -31,7 +31,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/articles/analysis.html b/docs/articles/analysis.html index d8b8656..f4a6e2e 100644 --- a/docs/articles/analysis.html +++ b/docs/articles/analysis.html @@ -31,7 +31,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 @@ -102,7 +102,7 @@

Data Analysis

Rob Gilmore & Shaurita Hutchins

-

2019-02-11

+

2019-02-13

Source: vignettes/analysis.Rmd @@ -355,7 +355,7 @@

# Generate heat_trees heat_tree_plots <- heat_tree_plots(metacoder_obj, rank_list = c("Phylum", "Class", "Order"), - node_label = ifelse(wilcox_p_value > 0.05, taxon_ids, NA), + node_label = ifelse(wilcox_p_value < 0.05, taxon_ids, NA), node_label_size = 2, node_label_color = c("darkgreen")) diff --git a/docs/articles/analysis_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/analysis_files/figure-html/unnamed-chunk-10-1.png index 8363fa3..0ef743f 100644 Binary files a/docs/articles/analysis_files/figure-html/unnamed-chunk-10-1.png and b/docs/articles/analysis_files/figure-html/unnamed-chunk-10-1.png differ diff --git a/docs/articles/analysis_files/figure-html/unnamed-chunk-11-1.png b/docs/articles/analysis_files/figure-html/unnamed-chunk-11-1.png index eac4f25..d0a133f 100644 Binary files a/docs/articles/analysis_files/figure-html/unnamed-chunk-11-1.png and b/docs/articles/analysis_files/figure-html/unnamed-chunk-11-1.png differ diff --git a/docs/articles/analysis_files/figure-html/unnamed-chunk-12-1.png b/docs/articles/analysis_files/figure-html/unnamed-chunk-12-1.png index 5b77d8b..7a64ac9 100644 Binary files a/docs/articles/analysis_files/figure-html/unnamed-chunk-12-1.png and b/docs/articles/analysis_files/figure-html/unnamed-chunk-12-1.png differ diff --git a/docs/articles/analysis_files/figure-html/unnamed-chunk-13-1.png b/docs/articles/analysis_files/figure-html/unnamed-chunk-13-1.png index 9da347b..5c838a0 100644 Binary files a/docs/articles/analysis_files/figure-html/unnamed-chunk-13-1.png and b/docs/articles/analysis_files/figure-html/unnamed-chunk-13-1.png differ diff --git a/docs/articles/analysis_files/figure-html/unnamed-chunk-13-2.png b/docs/articles/analysis_files/figure-html/unnamed-chunk-13-2.png index 5c56464..2da290e 100644 Binary files a/docs/articles/analysis_files/figure-html/unnamed-chunk-13-2.png and b/docs/articles/analysis_files/figure-html/unnamed-chunk-13-2.png differ diff --git a/docs/articles/analysis_files/figure-html/unnamed-chunk-13-3.png b/docs/articles/analysis_files/figure-html/unnamed-chunk-13-3.png index fa01e1e..ac66db2 100644 Binary files a/docs/articles/analysis_files/figure-html/unnamed-chunk-13-3.png and b/docs/articles/analysis_files/figure-html/unnamed-chunk-13-3.png differ diff --git a/docs/articles/analysis_files/figure-html/unnamed-chunk-13-4.png b/docs/articles/analysis_files/figure-html/unnamed-chunk-13-4.png index 9cce121..1448e8d 100644 Binary files a/docs/articles/analysis_files/figure-html/unnamed-chunk-13-4.png and b/docs/articles/analysis_files/figure-html/unnamed-chunk-13-4.png differ diff --git a/docs/articles/color-palettes.html b/docs/articles/color-palettes.html index 7222ba5..cd43ec5 100644 --- a/docs/articles/color-palettes.html +++ b/docs/articles/color-palettes.html @@ -31,7 +31,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 @@ -102,7 +102,7 @@

Using Color Palettes

Rob Gilmore & Shaurita Hutchins

-

2019-02-08

+

2019-02-13

Source: vignettes/color-palettes.Rmd diff --git a/docs/articles/color-palettes_files/figure-html/unnamed-chunk-1-1.png b/docs/articles/color-palettes_files/figure-html/unnamed-chunk-1-1.png index 2944635..9ff6517 100644 Binary files a/docs/articles/color-palettes_files/figure-html/unnamed-chunk-1-1.png and b/docs/articles/color-palettes_files/figure-html/unnamed-chunk-1-1.png differ diff --git a/docs/articles/color-palettes_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/color-palettes_files/figure-html/unnamed-chunk-2-1.png index f51fab1..5e90471 100644 Binary files a/docs/articles/color-palettes_files/figure-html/unnamed-chunk-2-1.png and b/docs/articles/color-palettes_files/figure-html/unnamed-chunk-2-1.png differ diff --git a/docs/articles/color-palettes_files/figure-html/unnamed-chunk-2-2.png b/docs/articles/color-palettes_files/figure-html/unnamed-chunk-2-2.png index 21265bc..7b2260a 100644 Binary files a/docs/articles/color-palettes_files/figure-html/unnamed-chunk-2-2.png and b/docs/articles/color-palettes_files/figure-html/unnamed-chunk-2-2.png differ diff --git a/docs/articles/color-palettes_files/figure-html/unnamed-chunk-3-1.png b/docs/articles/color-palettes_files/figure-html/unnamed-chunk-3-1.png index e128b94..8f45dba 100644 Binary files a/docs/articles/color-palettes_files/figure-html/unnamed-chunk-3-1.png and b/docs/articles/color-palettes_files/figure-html/unnamed-chunk-3-1.png differ diff --git a/docs/articles/color-palettes_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/color-palettes_files/figure-html/unnamed-chunk-4-1.png index 2e3c894..625b858 100644 Binary files a/docs/articles/color-palettes_files/figure-html/unnamed-chunk-4-1.png and b/docs/articles/color-palettes_files/figure-html/unnamed-chunk-4-1.png differ diff --git a/docs/articles/color-palettes_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/color-palettes_files/figure-html/unnamed-chunk-5-1.png index 5810a6d..84d5a72 100644 Binary files a/docs/articles/color-palettes_files/figure-html/unnamed-chunk-5-1.png and b/docs/articles/color-palettes_files/figure-html/unnamed-chunk-5-1.png differ diff --git a/docs/articles/data-wrangling.html b/docs/articles/data-wrangling.html index 1dacea2..c328685 100644 --- a/docs/articles/data-wrangling.html +++ b/docs/articles/data-wrangling.html @@ -31,7 +31,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 @@ -102,7 +102,7 @@

Data Wrangling

Robert Gilmore

-

2019-02-08

+

2019-02-13

Source: vignettes/data-wrangling.Rmd diff --git a/docs/articles/filtering.html b/docs/articles/filtering.html index 00aff20..ff7e455 100644 --- a/docs/articles/filtering.html +++ b/docs/articles/filtering.html @@ -31,7 +31,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 @@ -102,7 +102,7 @@

Filtering Data

Robert Gilmore

-

2019-02-08

+

2019-02-13

Source: vignettes/filtering.Rmd diff --git a/docs/articles/index.html b/docs/articles/index.html index 2cb5bd2..1fe953f 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -62,7 +62,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/articles/introduction.html b/docs/articles/introduction.html index 2010eab..dbe4b9a 100644 --- a/docs/articles/introduction.html +++ b/docs/articles/introduction.html @@ -31,7 +31,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 @@ -101,7 +101,7 @@

Introduction

-

2019-02-08

+

2019-02-13

Source: vignettes/introduction.Rmd diff --git a/docs/authors.html b/docs/authors.html index 64633a6..3001364 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -62,7 +62,7 @@ MicrobiomeR - 0.4.0 + 0.4.1
diff --git a/docs/index.html b/docs/index.html index 4ccf9a4..405269e 100644 --- a/docs/index.html +++ b/docs/index.html @@ -32,7 +32,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/news/index.html b/docs/news/index.html index 40f719a..3b97ea2 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -62,7 +62,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 @@ -135,6 +135,14 @@

Changelog

Source: NEWS.md +
+

+MicrobiomeR 0.4.1

+ +

MicrobiomeR 0.4.0

@@ -380,6 +388,7 @@

Contents

    +
  • 0.4.1
  • 0.4.0
  • 0.3.1
  • 0.3.0
    • diff --git a/docs/reference/MicrobiomeR.html b/docs/reference/MicrobiomeR.html index 3021d50..307ec62 100644 --- a/docs/reference/MicrobiomeR.html +++ b/docs/reference/MicrobiomeR.html @@ -66,7 +66,7 @@ MicrobiomeR - 0.4.0 + 0.4.1
diff --git a/docs/reference/MicrobiomeR_Formats.html b/docs/reference/MicrobiomeR_Formats.html index 02ae004..dada626 100644 --- a/docs/reference/MicrobiomeR_Formats.html +++ b/docs/reference/MicrobiomeR_Formats.html @@ -83,7 +83,7 @@ MicrobiomeR - 0.4.0 + 0.4.1

diff --git a/docs/reference/MicrobiomeR_Workflow.html b/docs/reference/MicrobiomeR_Workflow.html index 6b73645..80fcdee 100644 --- a/docs/reference/MicrobiomeR_Workflow.html +++ b/docs/reference/MicrobiomeR_Workflow.html @@ -66,7 +66,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/agglomerate_metacoder.html b/docs/reference/agglomerate_metacoder.html index 734acaa..4955ab6 100644 --- a/docs/reference/agglomerate_metacoder.html +++ b/docs/reference/agglomerate_metacoder.html @@ -67,7 +67,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/alpha_diversity_measures.html b/docs/reference/alpha_diversity_measures.html index b2a1c29..ef4250d 100644 --- a/docs/reference/alpha_diversity_measures.html +++ b/docs/reference/alpha_diversity_measures.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/alpha_diversity_plot.html b/docs/reference/alpha_diversity_plot.html index 0774d2e..2ae0474 100644 --- a/docs/reference/alpha_diversity_plot.html +++ b/docs/reference/alpha_diversity_plot.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/as_MicrobiomeR_format.html b/docs/reference/as_MicrobiomeR_format.html index 0352136..064e582 100644 --- a/docs/reference/as_MicrobiomeR_format.html +++ b/docs/reference/as_MicrobiomeR_format.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/as_analyzed_format.html b/docs/reference/as_analyzed_format.html index c295597..a71ae86 100644 --- a/docs/reference/as_analyzed_format.html +++ b/docs/reference/as_analyzed_format.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/as_basic_format.html b/docs/reference/as_basic_format.html index 6b8aeb0..fc4b61c 100644 --- a/docs/reference/as_basic_format.html +++ b/docs/reference/as_basic_format.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/as_custom_format.html b/docs/reference/as_custom_format.html index 00a40ef..e58f8fb 100644 --- a/docs/reference/as_custom_format.html +++ b/docs/reference/as_custom_format.html @@ -66,7 +66,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/as_phyloseq_format.html b/docs/reference/as_phyloseq_format.html index f10ce2f..de58da2 100644 --- a/docs/reference/as_phyloseq_format.html +++ b/docs/reference/as_phyloseq_format.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/as_raw_format.html b/docs/reference/as_raw_format.html index 130ff5d..75bdcec 100644 --- a/docs/reference/as_raw_format.html +++ b/docs/reference/as_raw_format.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/combination_palette.html b/docs/reference/combination_palette.html index 2bfe4c6..0239219 100644 --- a/docs/reference/combination_palette.html +++ b/docs/reference/combination_palette.html @@ -66,7 +66,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/correlation_data.html b/docs/reference/correlation_data.html index c327475..a59698e 100644 --- a/docs/reference/correlation_data.html +++ b/docs/reference/correlation_data.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/correlation_plot.html b/docs/reference/correlation_plot.html index f0a6fd2..9e336a3 100644 --- a/docs/reference/correlation_plot.html +++ b/docs/reference/correlation_plot.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/correlation_plots.html b/docs/reference/correlation_plots.html index 604f47f..e5d8f4e 100644 --- a/docs/reference/correlation_plots.html +++ b/docs/reference/correlation_plots.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/cov_filter.html b/docs/reference/cov_filter.html index c6e5b8b..2dbc889 100644 --- a/docs/reference/cov_filter.html +++ b/docs/reference/cov_filter.html @@ -66,7 +66,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/create_metacoder.html b/docs/reference/create_metacoder.html index 9c14d70..00c1ddf 100644 --- a/docs/reference/create_metacoder.html +++ b/docs/reference/create_metacoder.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/create_phyloseq.html b/docs/reference/create_phyloseq.html index a78885a..a8535f3 100644 --- a/docs/reference/create_phyloseq.html +++ b/docs/reference/create_phyloseq.html @@ -68,7 +68,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/create_pub_table.html b/docs/reference/create_pub_table.html index 757e21f..ef9ae1d 100644 --- a/docs/reference/create_pub_table.html +++ b/docs/reference/create_pub_table.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/get_color_palette.html b/docs/reference/get_color_palette.html index 4db3195..ec4409c 100644 --- a/docs/reference/get_color_palette.html +++ b/docs/reference/get_color_palette.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/heat_tree_parameters.html b/docs/reference/heat_tree_parameters.html index c724f5f..ee76b7f 100644 --- a/docs/reference/heat_tree_parameters.html +++ b/docs/reference/heat_tree_parameters.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/heat_tree_plots.html b/docs/reference/heat_tree_plots.html index a33ba7b..2abdc88 100644 --- a/docs/reference/heat_tree_plots.html +++ b/docs/reference/heat_tree_plots.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/index.html b/docs/reference/index.html index 411e129..0c2870c 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -62,7 +62,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/is_analyzed_format.html b/docs/reference/is_analyzed_format.html index ba8bd2c..e67ba51 100644 --- a/docs/reference/is_analyzed_format.html +++ b/docs/reference/is_analyzed_format.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/is_basic_format.html b/docs/reference/is_basic_format.html index 050d98e..2745441 100644 --- a/docs/reference/is_basic_format.html +++ b/docs/reference/is_basic_format.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/is_phyloseq_format.html b/docs/reference/is_phyloseq_format.html index 00e5a45..9842e26 100644 --- a/docs/reference/is_phyloseq_format.html +++ b/docs/reference/is_phyloseq_format.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/is_raw_format.html b/docs/reference/is_raw_format.html index 3bc0db9..ff17cd2 100644 --- a/docs/reference/is_raw_format.html +++ b/docs/reference/is_raw_format.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/metacoder_comp_func_1.html b/docs/reference/metacoder_comp_func_1.html index 5b1fcae..e0d0787 100644 --- a/docs/reference/metacoder_comp_func_1.html +++ b/docs/reference/metacoder_comp_func_1.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/order_metacoder_data.html b/docs/reference/order_metacoder_data.html index 8c3badc..c7f3620 100644 --- a/docs/reference/order_metacoder_data.html +++ b/docs/reference/order_metacoder_data.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/ordination_plot.html b/docs/reference/ordination_plot.html index cb26d56..7227196 100644 --- a/docs/reference/ordination_plot.html +++ b/docs/reference/ordination_plot.html @@ -66,7 +66,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/otu_id_filter.html b/docs/reference/otu_id_filter.html index 210771b..851ff41 100644 --- a/docs/reference/otu_id_filter.html +++ b/docs/reference/otu_id_filter.html @@ -66,7 +66,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/otu_prevalence_filter.html b/docs/reference/otu_prevalence_filter.html index 35df62d..d0bcb3e 100644 --- a/docs/reference/otu_prevalence_filter.html +++ b/docs/reference/otu_prevalence_filter.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/otu_proportion_filter.html b/docs/reference/otu_proportion_filter.html index 1e613ab..6307ad5 100644 --- a/docs/reference/otu_proportion_filter.html +++ b/docs/reference/otu_proportion_filter.html @@ -66,7 +66,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/output_dir.html b/docs/reference/output_dir.html index 6d36c71..5511655 100644 --- a/docs/reference/output_dir.html +++ b/docs/reference/output_dir.html @@ -66,7 +66,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/parse_taxonomy_silva_128.html b/docs/reference/parse_taxonomy_silva_128.html index f4ead43..db3623f 100644 --- a/docs/reference/parse_taxonomy_silva_128.html +++ b/docs/reference/parse_taxonomy_silva_128.html @@ -100,7 +100,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/permanova.html b/docs/reference/permanova.html index e2b2880..997675f 100644 --- a/docs/reference/permanova.html +++ b/docs/reference/permanova.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/phyloseq_silva_2.html b/docs/reference/phyloseq_silva_2.html index 822142c..f85e144 100644 --- a/docs/reference/phyloseq_silva_2.html +++ b/docs/reference/phyloseq_silva_2.html @@ -66,7 +66,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/phyloseq_silva_3.html b/docs/reference/phyloseq_silva_3.html index e950c81..aedd7f7 100644 --- a/docs/reference/phyloseq_silva_3.html +++ b/docs/reference/phyloseq_silva_3.html @@ -66,7 +66,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/pick_new_outgroup.html b/docs/reference/pick_new_outgroup.html index 9fbfc16..1169c4c 100644 --- a/docs/reference/pick_new_outgroup.html +++ b/docs/reference/pick_new_outgroup.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/pipe.html b/docs/reference/pipe.html index 6700da6..fea6fc7 100644 --- a/docs/reference/pipe.html +++ b/docs/reference/pipe.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/plot_limits.html b/docs/reference/plot_limits.html index 5eb8f53..046adc3 100644 --- a/docs/reference/plot_limits.html +++ b/docs/reference/plot_limits.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/raw_silva_2.html b/docs/reference/raw_silva_2.html index 46ba6f2..5c31d0e 100644 --- a/docs/reference/raw_silva_2.html +++ b/docs/reference/raw_silva_2.html @@ -67,7 +67,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/raw_silva_3.html b/docs/reference/raw_silva_3.html index bfb64a7..d3e6a13 100644 --- a/docs/reference/raw_silva_3.html +++ b/docs/reference/raw_silva_3.html @@ -67,7 +67,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/root_by_longest_edge.html b/docs/reference/root_by_longest_edge.html index b855dcb..db64c3d 100644 --- a/docs/reference/root_by_longest_edge.html +++ b/docs/reference/root_by_longest_edge.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/root_phyloseq_tree.html b/docs/reference/root_phyloseq_tree.html index 1bd260e..81e331f 100644 --- a/docs/reference/root_phyloseq_tree.html +++ b/docs/reference/root_phyloseq_tree.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/sample_id_filter.html b/docs/reference/sample_id_filter.html index 59c72e8..e3a59f7 100644 --- a/docs/reference/sample_id_filter.html +++ b/docs/reference/sample_id_filter.html @@ -66,7 +66,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/save_alpha_diversity_plots.html b/docs/reference/save_alpha_diversity_plots.html index 36d552f..26afbe0 100644 --- a/docs/reference/save_alpha_diversity_plots.html +++ b/docs/reference/save_alpha_diversity_plots.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/save_correlation_plots.html b/docs/reference/save_correlation_plots.html index c890d8a..2872722 100644 --- a/docs/reference/save_correlation_plots.html +++ b/docs/reference/save_correlation_plots.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/save_heat_tree_plots.html b/docs/reference/save_heat_tree_plots.html index ae56028..576a3d2 100644 --- a/docs/reference/save_heat_tree_plots.html +++ b/docs/reference/save_heat_tree_plots.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/save_ordination_plots.html b/docs/reference/save_ordination_plots.html index 936c20f..8d5d3b1 100644 --- a/docs/reference/save_ordination_plots.html +++ b/docs/reference/save_ordination_plots.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/save_stacked_barplots.html b/docs/reference/save_stacked_barplots.html index 65d0350..3f2d728 100644 --- a/docs/reference/save_stacked_barplots.html +++ b/docs/reference/save_stacked_barplots.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/save_top_coefficients_barplot.html b/docs/reference/save_top_coefficients_barplot.html index 2c3908f..71a344c 100644 --- a/docs/reference/save_top_coefficients_barplot.html +++ b/docs/reference/save_top_coefficients_barplot.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/scico_palette.html b/docs/reference/scico_palette.html index 4331913..88fe657 100644 --- a/docs/reference/scico_palette.html +++ b/docs/reference/scico_palette.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/stacked_barplot.html b/docs/reference/stacked_barplot.html index 54a4c07..b4c651a 100644 --- a/docs/reference/stacked_barplot.html +++ b/docs/reference/stacked_barplot.html @@ -66,7 +66,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/taxa_prevalence_filter.html b/docs/reference/taxa_prevalence_filter.html index eefb241..54c31b6 100644 --- a/docs/reference/taxa_prevalence_filter.html +++ b/docs/reference/taxa_prevalence_filter.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/taxon_id_filter.html b/docs/reference/taxon_id_filter.html index bbe0081..2edf80f 100644 --- a/docs/reference/taxon_id_filter.html +++ b/docs/reference/taxon_id_filter.html @@ -66,7 +66,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/top_coefficients_barplot.html b/docs/reference/top_coefficients_barplot.html index 284a47a..f1090e3 100644 --- a/docs/reference/top_coefficients_barplot.html +++ b/docs/reference/top_coefficients_barplot.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/transformer.html b/docs/reference/transformer.html index 60f16dc..9f9e808 100644 --- a/docs/reference/transformer.html +++ b/docs/reference/transformer.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/transposer.html b/docs/reference/transposer.html index 3e0d9e6..4842591 100644 --- a/docs/reference/transposer.html +++ b/docs/reference/transposer.html @@ -66,7 +66,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/treatment_matrix.html b/docs/reference/treatment_matrix.html index ea174f9..c461dd3 100644 --- a/docs/reference/treatment_matrix.html +++ b/docs/reference/treatment_matrix.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/validate_MicrobiomeR_format.html b/docs/reference/validate_MicrobiomeR_format.html index 27d11fb..b78e826 100644 --- a/docs/reference/validate_MicrobiomeR_format.html +++ b/docs/reference/validate_MicrobiomeR_format.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/viridis_magma_palette.html b/docs/reference/viridis_magma_palette.html index 9b36d14..2e1e096 100644 --- a/docs/reference/viridis_magma_palette.html +++ b/docs/reference/viridis_magma_palette.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/viridis_palette.html b/docs/reference/viridis_palette.html index 73522e5..3db142c 100644 --- a/docs/reference/viridis_palette.html +++ b/docs/reference/viridis_palette.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/vlookup.html b/docs/reference/vlookup.html index 0f205af..378bee7 100644 --- a/docs/reference/vlookup.html +++ b/docs/reference/vlookup.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/docs/reference/which_format.html b/docs/reference/which_format.html index a295c5d..7a90aa9 100644 --- a/docs/reference/which_format.html +++ b/docs/reference/which_format.html @@ -65,7 +65,7 @@ MicrobiomeR - 0.4.0 + 0.4.1 diff --git a/vignettes/analysis.Rmd b/vignettes/analysis.Rmd index 3b79b6e..d2dd7f1 100644 --- a/vignettes/analysis.Rmd +++ b/vignettes/analysis.Rmd @@ -268,7 +268,7 @@ metacoder_obj <- as_MicrobiomeR_format(obj = metacoder_obj, format = "analyzed_f # Generate heat_trees heat_tree_plots <- heat_tree_plots(metacoder_obj, rank_list = c("Phylum", "Class", "Order"), - node_label = ifelse(wilcox_p_value > 0.05, taxon_ids, NA), + node_label = ifelse(wilcox_p_value < 0.05, taxon_ids, NA), node_label_size = 2, node_label_color = c("darkgreen"))