miaViz
2 January 2022
Contents
miaViz implements plotting function to work with TreeSummarizedExperiment
and related objects in a context of microbiome analysis. For more general
plotting function on SummarizedExperiment objects the scater package offers
several options, such as plotColData, plotExpression and plotRowData.
1 Installation
To install miaViz, install BiocManager first, if it is not installed.
Afterwards use the install function from BiocManager and load miaViz.
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("miaViz")library(miaViz)
data(GlobalPatterns, package = "mia")2 Abundance plotting
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.
plotAbundance(GlobalPatterns, rank = NULL,
features = "549322", abund_values = "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).
GlobalPatterns <- transformCounts(GlobalPatterns, method = "relabundance")plotAbundance(GlobalPatterns, rank = "Kingdom", abund_values = "relabundance")
With subsetting to selected features the plot can be fine tuned.
prev_phylum <- getPrevalentTaxa(GlobalPatterns, rank = "Phylum",
detection = 0.01)plotAbundance(GlobalPatterns[rowData(GlobalPatterns)$Phylum %in% prev_phylum],
rank = "Phylum",
abund_values = "relabundance")
The features argument is reused for plotting data along the different samples.
In the next example the SampleType is plotted along the samples. In this case
the result is a list, which can combined using external tools, for example
patchwork.
library(patchwork)
plots <- plotAbundance(GlobalPatterns[rowData(GlobalPatterns)$Phylum %in% prev_phylum],
features = "SampleType",
rank = "Phylum",
abund_values = "relabundance")
plots$abundance / plots$SampleType +
plot_layout(heights = c(9, 1))
Further example about composition barplot can be found at Orchestrating Microbiome Analysis (Lahti, Shetty, and Ernst 2021).
3 Prevalence plotting
To visualize prevalence within the dataset, two functions are available,
plotTaxaPrevalence, plotPrevalenceAbundance and plotPrevalence.
plotTaxaPrevalence produces a so-called landscape plot, which
visualizes the prevalence of samples across abundance thresholds.
plotTaxaPrevalence(GlobalPatterns, rank = "Phylum",
detections = c(0, 0.001, 0.01, 0.1, 0.2))
plotPrevalenceAbundance plot the prevalence depending on the mean relative
abundance on the chosen taxonomic level.
plotPrevalentAbundance(GlobalPatterns, rank = "Family",
colour_by = "Phylum") +
scale_x_log10()
plotPrevalence plot the number of samples and their prevalence across
different abundance thresholds. Abundance steps can be adjusted using the
detections argument, whereas the analyzed prevalence steps is set using the
prevalences argument.
plotPrevalence(GlobalPatterns,
rank = "Phylum",
detections = c(0.01, 0.1, 1, 2, 5, 10, 20)/100,
prevalences = seq(0.1, 1, 0.1))
4 Tree plotting
The information stored in the rowTree can be directly plotted. However,
sizes of stored trees have to be kept in mind and plotting of large trees
rarely makes sense.
For this example we limit the information plotted to the top 100 taxa as judged by mean abundance on the genus level.
library(scater)
library(mia)altExp(GlobalPatterns,"Genus") <- agglomerateByRank(GlobalPatterns,"Genus")
altExp(GlobalPatterns,"Genus") <- addPerFeatureQC(altExp(GlobalPatterns,"Genus"))
rowData(altExp(GlobalPatterns,"Genus"))$log_mean <-
log(rowData(altExp(GlobalPatterns,"Genus"))$mean)
rowData(altExp(GlobalPatterns,"Genus"))$detected <-
rowData(altExp(GlobalPatterns,"Genus"))$detected / 100
top_taxa <- getTopTaxa(altExp(GlobalPatterns,"Genus"),
method="mean",
top=100L,
abund_values="counts")Colour, size and shape of tree tips and nodes can be decorated based on data
present in the SE object or by providing additional information via the
other_fields argument. Note that currently information for nodes have to be
provided via the other_fields arguments.
Data will be matched via the node or label argument depending on which was
provided. label takes precedent.
plotRowTree(altExp(GlobalPatterns,"Genus")[top_taxa,],
tip_colour_by = "log_mean",
tip_size_by = "detected")
#> Warning in .numeric_ij(ij = i, x = x, dim = "row"): For rows/cols with the same
#> name, only one is output
#> Warning in convertNode(tree = track, node = oldAlias): Multiple nodes are found
#> to have the same label.
#> Warning in convertNode(tree = value, node = nlk$nodeLab[iRep]): Multiple nodes
#> are found to have the same label.
Figure 1: Tree plot using ggtree with tip labels decorated by mean abundance (colour) and prevalence (size)
Tip and node labels can be shown as well. Setting show_label = TRUE shows the
tip labels only …
plotRowTree(altExp(GlobalPatterns,"Genus")[top_taxa,],
tip_colour_by = "log_mean",
tip_size_by = "detected",
show_label = TRUE)
#> Warning in .numeric_ij(ij = i, x = x, dim = "row"): For rows/cols with the same
#> name, only one is output
#> Warning in convertNode(tree = track, node = oldAlias): Multiple nodes are found
#> to have the same label.
#> Warning in convertNode(tree = value, node = nlk$nodeLab[iRep]): Multiple nodes
#> are found to have the same label.
Figure 2: Tree plot using ggtree with tip labels decorated by mean abundance (colour) and prevalence (size)
Tip labels of the tree are shown as well.
… whereas node labels can be selectively shown by providing a named logical
vector to show_label.
Please not that currently ggtree only can plot node labels in a rectangular
layout.
labels <- c("Genus:Providencia", "Genus:Morganella", "0.961.60")
plotRowTree(altExp(GlobalPatterns,"Genus")[top_taxa,],
tip_colour_by = "log_mean",
tip_size_by = "detected",
show_label = labels,
layout="rectangular")
#> Warning in .numeric_ij(ij = i, x = x, dim = "row"): For rows/cols with the same
#> name, only one is output
#> Warning in convertNode(tree = track, node = oldAlias): Multiple nodes are found
#> to have the same label.
#> Warning in convertNode(tree = value, node = nlk$nodeLab[iRep]): Multiple nodes
#> are found to have the same label.
Figure 3: Tree plot using ggtree with tip labels decorated by mean abundance (colour) and prevalence (size)
Selected node and tip labels are shown.
Information can also be visualized on the edges of the tree plot.
plotRowTree(altExp(GlobalPatterns,"Genus")[top_taxa,],
edge_colour_by = "Phylum",
tip_colour_by = "log_mean")
#> Warning in .numeric_ij(ij = i, x = x, dim = "row"): For rows/cols with the same
#> name, only one is output
#> Warning in convertNode(tree = track, node = oldAlias): Multiple nodes are found
#> to have the same label.
#> Warning in convertNode(tree = value, node = nlk$nodeLab[iRep]): Multiple nodes
#> are found to have the same label.
Figure 4: Tree plot using ggtree with tip labels decorated by mean abundance (colour) and edges labeled Kingdom (colour) and prevalence (size)
5 Graph plotting
Similar to tree data, graph data can also be plotted in conjunction with
SummarizedExperiment objects. Since the graph data in itself cannot be stored
in a specialized slot, a graph object can be provided separately or as an
element from the metedata.
Here we load an example graph. As graph data, all objects types accepted by
as_tbl_graph from the tidygraph package are supported.
data(col_graph)In the following examples, the weight data is automatically generated from the
graph data. The SummarizedExperiment provided is required to have overlapping
rownames with the node names of the graph. Using this link the graph plot
can incorporated data from the SummarizedExperiment.
plotColGraph(col_graph,
altExp(GlobalPatterns,"Genus"),
colour_by = "SampleType",
edge_colour_by = "weight",
edge_width_by = "weight",
show_label = TRUE)
As mentioned the graph data can be provided from the metadata of the
SummarizedExperiment.
metadata(altExp(GlobalPatterns,"Genus"))$graph <- col_graphThis produces the same plot as shown above.
6 Plotting of serial data
library(microbiomeDataSets)
silverman <- SilvermanAGutData()
#> snapshotDate(): 2021-10-19
#> see ?microbiomeDataSets and browseVignettes('microbiomeDataSets') for documentation
#> loading from cache
#> see ?microbiomeDataSets and browseVignettes('microbiomeDataSets') for documentation
#> loading from cache
#> see ?microbiomeDataSets and browseVignettes('microbiomeDataSets') for documentation
#> loading from cache
#> see ?microbiomeDataSets and browseVignettes('microbiomeDataSets') for documentation
#> loading from cache
#> see ?microbiomeDataSets and browseVignettes('microbiomeDataSets') for documentation
#> loading from cache
silverman <- transformCounts(silverman, method = "relabundance")
taxa <- getTopTaxa(silverman, 2)Data from samples collected along time can be visualized using plotSeries.
The x argument is used to reference data from the colData to use as
descriptor for ordering the data. The y 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.
plotSeries(silverman,
x = "DAY_ORDER",
y = taxa,
colour_by = "Family")
If replicated data is present, data is automatically used for calculation of the
mean and sd and plotted as a range. Data from different assays can be used
for plotting via the abund_values.
plotSeries(silverman[taxa,],
x = "DAY_ORDER",
colour_by = "Family",
linetype_by = "Phylum",
abund_values = "relabundance")
Additional variables can be used to modify line type aesthetics.
plotSeries(silverman,
x = "DAY_ORDER",
y = getTopTaxa(silverman, 5),
colour_by = "Family",
linetype_by = "Phylum",
abund_values = "counts")
7 Plotting factor data
To visualize the relative relations between two groupings among the factor data,
two functions are available for the purpose; plotColTile and plotRowTile.
data(GlobalPatterns)
se <- GlobalPatterns
plotColTile(se,"SampleType","Primer") +
theme(axis.text.x.top = element_text(angle = 45, hjust = 0))
8 DMN fit plotting
Searching for groups that are similar to each other among the samples, could be
approached with the Dirichlet Multinomial Mixtures (Holmes, Harris, and Quince 2012).
After using runDMN from the mia package, several k values as a number of clusters
are used to observe the best fit (see also getDMN 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"
# plot the fit
plotDMNFit(dmn_se, type = "laplace")
More examples and materials are available at Orchestrating Microbiome Analysis (Lahti, Shetty, and Ernst 2021).
9 Session info
sessionInfo()
#> R version 4.1.2 (2021-11-01)
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#> Running under: Ubuntu 20.04.3 LTS
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#> BLAS: /home/biocbuild/bbs-3.14-bioc/R/lib/libRblas.so
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#>
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#> attached base packages:
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#> [1] microbiomeDataSets_1.2.0 scater_1.22.0
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#> [5] miaViz_1.2.1 ggraph_2.0.5
#> [7] ggplot2_3.3.5 mia_1.2.3
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#> [129] ggbeeswarm_0.6.0References
Holmes, Ian, Keith Harris, and Christopher Quince. 2012. “Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics.” PLOS ONE. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030126.
Lahti, Leo, Sudarshan Shetty, and Felix GM Ernst. 2021. “Orchestrating Microbiome Analysis.” https://microbiome.github.io/OMA/.