Plot feature loadings function (#135)

Co-authored-by: seraidarian <[email protected]> Co-authored-by: Leo Lahti <[email protected]> Co-authored-by: Tuomas Borman <[email protected]> Co-authored-by: TuomasBorman <[email protected]>
microbiome · Aug 13, 2024 · 1217307 · 1217307
1 parent 102c876
commit 1217307
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: miaViz
 Title: Microbiome Analysis Plotting and Visualization
-Version: 1.13.9
+Version: 1.13.10
 Authors@R: 
     c(person(given = "Tuomas", family = "Borman", role = c("aut", "cre"),
              email = "[email protected]",
@@ -50,6 +50,7 @@ Imports:
     ggnewscale,
     viridis,
     tibble,
+    tidytext,
     tidytree,
     tidygraph,
     rlang,

diff --git a/NAMESPACE b/NAMESPACE
@@ -6,6 +6,7 @@ export(plotColGraph)
 export(plotColTile)
 export(plotDMNFit)
 export(plotFeaturePrevalence)
+export(plotLoadings)
 export(plotNMDS)
 export(plotPrevalence)
 export(plotPrevalentAbundance)
@@ -28,6 +29,7 @@ exportMethods(plotColTile)
 exportMethods(plotColTree)
 exportMethods(plotDMNFit)
 exportMethods(plotFeaturePrevalence)
+exportMethods(plotLoadings)
 exportMethods(plotPrevalence)
 exportMethods(plotPrevalentAbundance)
 exportMethods(plotRDA)
@@ -91,11 +93,14 @@ importFrom(ggplot2,geom_bar)
 importFrom(ggplot2,geom_line)
 importFrom(ggplot2,geom_point)
 importFrom(ggplot2,geom_raster)
+importFrom(ggplot2,geom_tile)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,labs)
 importFrom(ggplot2,scale_colour_manual)
 importFrom(ggplot2,scale_fill_distiller)
+importFrom(ggplot2,scale_fill_gradient2)
 importFrom(ggplot2,scale_fill_manual)
+importFrom(ggplot2,scale_fill_viridis_d)
 importFrom(ggplot2,scale_size_identity)
 importFrom(ggplot2,scale_x_continuous)
 importFrom(ggplot2,scale_x_discrete)
@@ -114,6 +119,7 @@ importFrom(ggtree,geom_tiplab)
 importFrom(ggtree,geom_tippoint)
 importFrom(ggtree,geom_tree)
 importFrom(ggtree,ggtree)
+importFrom(ggtree,gheatmap)
 importFrom(ggtree,groupOTU)
 importFrom(ggtree,theme_tree)
 importFrom(mia,meltSE)
@@ -133,6 +139,8 @@ importFrom(tidygraph,as_tbl_graph)
 importFrom(tidygraph,as_tibble)
 importFrom(tidyr,drop_na)
 importFrom(tidyr,pivot_longer)
+importFrom(tidytext,reorder_within)
+importFrom(tidytext,scale_y_reordered)
 importFrom(tidytree,as.phylo)
 importFrom(tidytree,as.treedata)
 importFrom(tidytree,as_tibble)

diff --git a/NEWS b/NEWS
@@ -32,3 +32,4 @@ Changes in version 1.13.x
 + Added getNeatOrder function
 + plotAbundance: enable plotting without agglomeration
 + Change parameter naming convention from parameter_name to parameter.name
++ Added plotLoadings function