Merge pull request #78 from vallenderlab/quick-fix

Quick fixes and update to 0.4.1
vallenderlab · Feb 14, 2019 · 095a03c · 095a03c
2 parents 9dca8bf + eb2c0b0
commit 095a03c
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diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html
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