Panel Catalogue
11 March 2025
Package
iSEEtree 1.1.3
1 Introduction
This page introduces users to the complete catalogue of panels provided by iSEEtree. Each panel is presented individually and visualised as it appears in the app. This catalogue is divided into four sections:
- compositional analysis: abundance plot, abundance density plot, prevalence plot and complex heatmap plot
- ordination analysis: RDA plot, Scree plot, loading plot and reduced dimension plot
- structural analysis: row/column tree plots and row/column graph plots
- other: row/column tile plots, mediation plot and row/column data plots
2 Compositional Analysis
| Panel name | Panel class | Purpose |
|---|---|---|
| Abundance plot | AbundancePlot | Feature composition by sample |
| Abundance density plot | AbundanceDensityPlot | Feature distribution across samples |
| Prevalence plot | PrevalencePlot | Feature prevalence across samples |
| Complex heatmap plot | ComplexHeatmapPlot | Whole assay composition |
2.1 Abundance plot
The Abundance plot illustrates the feature composition of each sample with a barplot of the relative or absolute feature abundace. This panel is based on the miaViz function plotAbundance.
Supported operations:
- Selecting taxonomic rank of the composition
- Choosing either absolute or relative abundance
- Ordering samples by feature or sample metadata
- Customising aesthetics
2.2 Abundance density plot
The Abundance density plot provides an alternative way to visualise abundance. In this panel, each row represents the feature distribution across the samples. It is based on the miaViz function plotAbundanceDensity.
Supported operations:
- selecting layout (jitter, density or dot plot)
- specifying the number of top features to show
- customising aesthetics
2.3 Prevalence plot
Coming soon!
2.4 Complex heatmap plot
3 Ordination Analysis
| Panel name | Panel class | Purpose |
|---|---|---|
| RDA plot | RDAPlot | Supervised ordination |
| Scree plot | ScreePlot | Explained variance by component |
| Loading plot | LoadingPlot | Feature loadings by component |
| Reduced dimension plot | ReducedDimensionPlot | Any ordination result |
3.1 RDA plot
The RDA plot visualises results for a distance-based Redundance Analysis (dbRDA) performed on a TreeSE object with the mia function runRDA. It is based on the miaViz function plotRDA.
Supported operations:
- selecting reduced dimension
- adjusting statistical parameters
- customising aesthetics
3.2 Scree plot
The Scree plot shows the proportion of variance explained by each component of a dimensionality reduction analysis by means of a line plot or barplot. It is based on the miaViz function plotScree.
Supported operations:
- selecting reduced dimension
- changing number of components
- showing individual or cumulative variance
- adding components labels and names
3.3 Loading plot
The Loading plot visualises the contributions of each feature to the components of a reduced dimension of choice. It is based on the miaViz function plotLoadings.
Supported operations:
- selecting layout (barplot, heatmap or lollipop)
- changing number of components
- adding feature tree
3.4 Reduced dimension plot
The Reduced dimension plot is inherited from iSEE. It is based on the scater function plotReducedDim and and can be used to visualise the results of an ordination analysis with both supervised and unsupervised methods as dot plot with reduced dimensions as coordinate axes.
4 Structural Analysis
| Panel name | Panel class | Purpose |
|---|---|---|
| Row tree plot | RowTreePlot | Hierarchical structure of features |
| Column tree plot | ColumnTreePlot | Hierarchical structure of samples |
| Row graph plot | RowGraphPlot | Network structure of features |
| Column graph plot | ColumnGraphPlot | Network structure of samples |
4.1 Row/Column tree plots
Row and column tree plots belong to the TreePlot family. They can be used to visualise the hierarchical organisation of the features or samples by means of a tree. They are based on the miaViz functions plotRowTree and plotColTree.
Supported operations:
- collapsing and expanding clades
- rotating and opening trees
- ordering trees
- labeling nodes and tips
- selecting tree layout
- customising aesthetics
4.2 Row/Column graph plots
Row and column graph plots belong to the GraphPlot family. They can be used to visualise the network organisation of the features or samples by means of a graph. They are based on the miaViz functions plotRowGraph and plotColGraph.
Supported operations:
- selecting graph and assay type
- labelling nodes
- selecting graph layout
- selecting edge type
- customising aesthetics
5 Other panels
| Panel name | Panel class | Purpose |
|---|---|---|
| Row tile plot | RowTreePlot | Variable distribution across feature groups |
| Column tile plot | ColumnTreePlot | Variable distribution across sample groups |
| Mediation plot | MediationPlot | Results of mediation analysis |
| Row data plot | RowDataPlot | Variables from feature metadata |
| Column data plot | ColumnDataPlot | Variables from sample metadata |
5.1 Row/Column tile plots
Coming soon!
5.2 Mediation plot
Coming soon!
5.3 Row/Column data plots
The Row and column data plots are inherited from iSEE. They are based on the scater functions plotRowData and plotColData and can be used to visualise feature or sample metadata as scatter plots when the x variable is continuous or boxplots when the x variable is discrete.
6 Reproducibility
R session information:
#> R Under development (unstable) (2025-02-19 r87757)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.2 LTS
#>
#> Matrix products: default
#> BLAS: /home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0 LAPACK version 3.12.0
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_GB LC_COLLATE=C
#> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
#> [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> time zone: America/New_York
#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats4 stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
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#> [4] mia_1.15.25 TreeSummarizedExperiment_2.15.0 Biostrings_2.75.4
#> [7] XVector_0.47.2 MultiAssayExperiment_1.33.9 iSEEtree_1.1.3
#> [10] iSEE_2.19.3 SingleCellExperiment_1.29.2 SummarizedExperiment_1.37.0
#> [13] Biobase_2.67.0 GenomicRanges_1.59.1 GenomeInfoDb_1.43.4
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#> [19] generics_0.1.3 MatrixGenerics_1.19.1 matrixStats_1.5.0
#> [22] RefManageR_1.4.0 BiocStyle_2.35.0
#>
#> loaded via a namespace (and not attached):
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#> [101] htmlwidgets_1.6.4 S4Arrays_1.7.3 pkgconfig_2.0.3 gtable_0.3.6
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#> [169] ape_5.8-1