fix issue 88 plotAbundance rank

R/plotAbundance.R

@@ -140,7 +140,6 @@ setGeneric("plotAbundance", signature = c("x"),
     }
 }
 
-
 #' @rdname plotAbundance
 #' @importFrom scater plotExpression
 #' @importFrom ggplot2 facet_wrap
@@ -164,36 +163,31 @@ setMethod("plotAbundance", signature = c("SummarizedExperiment"),
             stop("No data to plot. nrow(x) == 0L.", call. = FALSE)
         }
         .check_assay_present(assay.type, x)
-        # if rank is set to NULL, default to plotExpression 
-        if(is.null(rank)){
-            plot <- plotExpression(x, features = features, 
-                                exprs_values = assay.type,
-                                one_facet = one_facet,
-                                ncol = ncol, scales = scales, ...)
-            ylab <- gsub("Expression","Abundance",plot$labels$y)
-            plot <- plot +
-                ylab(ylab)
-            return(plot)
-        }
         ############################# INPUT CHECK #############################
-        if(!.is_non_empty_string(rank)){
-            stop("'rank' must be an non empty single character value.",
+        if(!.is_non_empty_string(rank) && !is.null(rank)){
+            stop("'rank' must be an non empty single character value or NULL.",
                 call. = FALSE)
         }
         if(!.is_a_bool(use_relative)){
             stop("'use_relative' must be TRUE or FALSE.",
                 call. = FALSE)
         }
-        .check_taxonomic_rank(rank, x)
+        if(!is.null(rank)){
+            .check_taxonomic_rank(rank, x)
+        }
         .check_for_taxonomic_data_order(x)
         layout <- match.arg(layout, c("bar","point"))
         order_rank_by <- match.arg(order_rank_by, c("name","abund","revabund"))
         .check_abund_plot_args(one_facet = one_facet,
                             ncol = ncol)
-        if( !is.null(features) ){
+        if( !is.null(features) & !is.null(rank) ){
             features <- match.arg(features, colnames(colData(x)))
         }
         ########################### INPUT CHECK END ###########################
+        if(is.null(rank)){
+           rank <- "Feature"
+           rowData(x)[[ rank ]] <- rownames(x)
+        }
         abund_data <- .get_abundance_data(x, rank, assay.type, order_rank_by,
                                         use_relative)
         order_sample_by <- .norm_order_sample_by(order_sample_by,

vignettes/miaViz.Rmd

@@ -40,27 +40,25 @@ BiocManager::install("miaViz")
 
 ```{r setup, message=FALSE}
 library(miaViz)
+library(scater)
 data(GlobalPatterns, package = "mia")
 ```
 
 # Abundance plotting
 
-in contrast to other fields of sequencing based fields of research for which
+In contrast to other fields of sequencing based fields of research for which
 expression of genes is usually studied, microbiome research uses the more 
 term ~Abundance~ to described the numeric data measured and analyzed.
 Technically, especially in context of `SummarizedExperiment` objects, there is
-no difference. Therefore `plotExpression` can be used to plot `Abundance` data.
-
-`plotAbundance` can be used as well and as long as `rank` is set `NULL`, it
-behaves as `plotExpression`.
+no difference. Therefore `plotExpression` can be used to plot `Abundance` data of a particular feature.
 
 ```{r}
-plotAbundance(GlobalPatterns, rank = NULL, 
+plotExpression(GlobalPatterns, 
               features = "549322", assay.type = "counts")
 ```
 
-However, if the `rank` is set not `NULL` a bar plot is returned. At the same
-time the `features` argument can be set to `NULL` (default).
+On the other hand, plotAbundance can be used to plot abundance by  `rank`. A bar plot is returned showing the relative abundance within each sample for a given `rank`. At the same
+time the `features` argument can be set to `NULL` (default). 
 
 ```{r}
 GlobalPatterns <- transformAssay(GlobalPatterns, method = "relabundance")
@@ -70,6 +68,13 @@ GlobalPatterns <- transformAssay(GlobalPatterns, method = "relabundance")
 plotAbundance(GlobalPatterns, rank = "Kingdom", assay.type = "relabundance")
 ```
 
+If `rank`is set to null however then the bars will be colored by each individual taxon. Please note that if you're doing this make sure to agglomerate your data to a certain taxonomic hand before plotting.
+
+```{r}
+GlobalPatterns.agglomerated <- agglomerateByRank(GlobalPatterns, 'Kingdom')
+plotAbundance(GlobalPatterns.agglomerated, rank = NULL, assay.type = "relabundance")
+```
+
 With subsetting to selected features the plot can be fine tuned.
 
 ```{r}