```{css, echo=FALSE} pre code { white-space: pre !important; overflow-x: scroll !important; word-break: keep-all !important; word-wrap: initial !important; }

```r
## ThG: chunk added to enable global knitr options. The below turns on
## caching for faster vignette re-build during text editing.
knitr::opts_chunk$set(cache=TRUE)
library(knitr); opts_chunk$set(message=FALSE, warning=FALSE)

Introduction

Motivation

The spatialHeatmap package provides functionalities for visualizing cell-, tissue- and organ-specific data of biological assays by coloring the corresponding spatial features defined in anatomical images according to quantitative abundance levels of measured biomolecules, such as transcripts, proteins or metabolites [@shm]. A color key is used to represent the quantitative assay values and can be customized by the user. This core functionality of the package is called a spatial heatmap (SHM) plot. Additional important functionalities include Spatial Enrichment (SE), Spatial Co-Expression (SCE), and Single Cell to SHM Co-Visualization (SC2SHM-CoViz). These extra utilities are useful for identifying biomolecules with spatially selective abundance patterns (SE), groups of biomolecules with related abundance profiles using hierarchical clustering, K-means clustering, or network analysis (SCE), and to co-visualize single cell embedding results with SHMs (SCSHM-CoViz). The latter co-visualization functionality (Figure \@ref(fig:illus)E) is described in a separate vignette called SCSHM-CoViz{target='_blank'}.

The functionalities of spatialHeatmap can be used either in a command-driven mode from within R or a graphical user interface (GUI) provided by a Shiny App that is part of this project. While the R-based mode provides flexibility to customize and automate analysis routines, the Shiny App includes a variety of convenience features that will appeal to experimentalists and users less familiar with R. The Shiny App can be used on both local computers as well as centralized server-based deployments (e.g. cloud-based or custom servers). This way it can be used for both hosting community data on a public server or running on a private system. The core functionalities of the spatialHeatmap package are illustrated in Figure \@ref(fig:illus).

include_graphics('img/graphical_overview_shm.jpg')

The package supports anatomical images from public repositories or those provided by users. In general any type of image can be used as long as it can be provided in SVG (Scalable Vector Graphics) format and the corresponding spatial features, such as organs, tissues, cellular compartments, are annotated (see aSVG below). The numeric values plotted onto an SHM are usually quantitative measurements from a wide range of profiling technologies, such as microarrays, next generation sequencing (e.g. RNA-Seq and scRNA-Seq), proteomics, metabolomics, or many other small- or large-scale experiments. For convenience, several preprocessing and normalization methods for the most common use cases are included that support raw and/or preprocessed data. Currently, the main application domains of the spatialHeatmap package are numeric data sets and spatially mapped images from biological, agricultural and biomedical areas. Moreover, the package has been designed to also work with many other spatial data types, such as population data plotted onto geographic maps. This high level of flexibility is one of the unique features of spatialHeatmap. Related software tools for biological applications in this field are largely based on pure web applications [@Maag2018-gi; @Lekschas2015-gd; @Papatheodorou2018-jy; @Winter2007-bq; @Waese2017-fx] or local tools [@Muschelli2014-av] that typically lack customization functionalities. These restrictions limit users to utilizing pre-existing expression data and/or fixed sets of anatomical image collections. To close this gap for biological use cases, we have developed spatialHeatmap as a generic R/Bioconductor package for plotting quantitative values onto any type of spatially mapped images in a programmable environment and/or in an intuitive to use GUI application.

Design {#design}

The core feature of spatialHeatmap is to map assay values (e.g. gene expression data) of one or many biomolecules (e.g. genes) measured under different conditions in form of numerically graded colors onto the corresponding cell types or tissues represented in a chosen SVG image. In the gene profiling field, this feature supports comparisons of the expression values among multiple genes by plotting their SHMs next to each other. Similarly, one can display the expression values of a single or multiple genes across multiple conditions in the same plot (Figure \@ref(fig:mul)). This level of flexibility is very efficient for visualizing complicated expression patterns across genes, cell types and conditions. In case of more complex anatomical images with overlapping multiple layer tissues, it is important to visually expose the tissue layer of interest in the plots. To address this, several default and customizable layer viewing options are provided. They allow to hide features in the top layers by making them transparent in order to expose features below them. This transparency viewing feature is highlighted below in the mouse example (Figure \@ref(fig:musshm)). Moreover, one can plot multiple distinct aSVGs in a single SHM plot as shown in Figure \@ref(fig:arabshm). This is particularly useful for displaying abundance trends across multiple development stages, where each is represented by its own aSVG image. In addition to static SHM representations, one can visualize them in form of interactive HTML files or videos.

To maximize reusability and extensibility, the package organizes large-scale omics assay data along with the associated experimental design information in a SummarizedExperiment object [Figure \@ref(fig:illus)A; @se]. The latter is one of the core S4 classes within the Bioconductor ecosystem that has been widely adapted by many other software packages dealing with gene-, protein- and metabolite-level profiling data. In case of gene expression data, the assays slot of the SummarizedExperiment container is populated with a gene expression matrix, where the rows and columns represent the genes and tissue/conditions, respectively. The colData slot contains experimental design definitions including replicate and treatment information. The tissues and/or cell type information in the object maps via colData to the corresponding features in the SVG images using unique identifiers for the spatial features (e.g. tissues or cell types). This allows to color the features of interest in an SVG image according to the numeric data stored in a SummarizedExperiment object. For simplicity the numeric data can also be provided as numeric vectors or data.frames. This can be useful for testing purposes and/or the usage of simple data sets that may not require the more advanced features of the SummarizedExperiment class, such as measurements with only one or a few data points. The details about how to access the SVG images and properly format the associated expression data are provided in the Supplementary Section of this vignette.

Image Format: SVG {#term}

SHMs are images where colors encode numeric values in features of any shape. For plotting SHMs, Scalable Vector Graphics (SVG) has been chosen as image format since it is a flexible and widely adapted vector graphics format that provides many advantages for computationally embedding numerical and other information in images. SVG is based on XML formatted text describing all components present in images, including lines, shapes and colors. In case of biological images suitable for SHMs, the shapes often represent anatomical or cell structures. To assign colors to specific features in SHMs, annotated SVG (aSVG) files are used where the shapes of interest are labeled according to certain conventions so that they can be addressed and colored programmatically. One or multiple aSVG files can be parsed and stored in the SVG S4 container with utilities provided by the spatialHeatmap package (Figure \@ref(fig:illus)B). The main slots of SVG include coordinate, attribute, dimension, svg, and raster. They correspond to feature coordinates, styling attributes (color, line width, etc.), width and heigth, original aSVG instances, and raster image paths, respectively. Raster images are required only when including photographic image components in SHMs (Figure \@ref(fig:overCol)), which is optional. Detailed instruction for creating custom aSVGs is provied in a separate tutorial{target='_blank'}.

SVGs and aSVGs of anatomical structures can be downloaded from many sources including the repositories described below. Alternatively, users can generate them themselves with vector graphics software such as Inkscape. Typically, in aSVGs one or more shapes of a feature of interest, such as the cell shapes of an organ, are grouped together by a common feature identifier. Via these group identifiers one or many feature types can be colored simultaneously in an aSVG according to biological experiments assaying the corresponding feature types with the required spatial resolution. To color spatial features according to numeric assay values, common identifiers are required for spatial features between the assay data and aSVGs. The color gradient used to visually represent the numeric assay values is controlled by a color gradient parameter. To visually interpret the meaning of the colors, the corresponding color key is included in the SHM plots. Additional details for properly formatting and annotating both aSVG images and assay data are provided in the Supplementary Section section of this vignette.

Data Repositories {#data_repo}

If not generated by the user, SHMs can be generated with data downloaded from various public repositories. This includes gene, protein and metabolic profiling data from databases, such as GEO{target='_blank'}, BAR{target='_blank'} and Expression Atlas{target='_blank'} from EMBL-EBI [@Papatheodorou2018-jy]. A particularly useful resource, when working with spatialHeatmap, is the EBI Expression Atlas. This online service contains both assay and anatomical images. Its assay data include mRNA and protein profiling experiments for different species, tissues and conditions. The corresponding anatomical image collections are also provided for a wide range of species including animals and plants. In spatialHeatmap several import functions are provided to work with the expression and aSVG repository from the Expression Atlas directly. The aSVG images developed by the spatialHeatmap project are available in its own repository called spatialHeatmap aSVG Repository{target='_blank'}, where users can contribute their aSVG images that are formatted according to our guidlines.

Tutorial Overview {#sample_data}

The following sections of this vignette showcase the most important functionalities of the spatialHeatmap package using as initial example a simple to understand testing data set, and then more complex mRNA profiling data from the Expression Atlas and GEO databases. The co-visualization functionality is explained in a separate vignette (see SCSHM-CoViz{target='_blank'}). First, SHM plots are generated for both the testing and mRNA expression data. The latter include gene expression data sets from RNA-Seq and microarray experiments of Human Brain, Mouse Organs, Chicken Organs, and Arabidopsis Shoots. The first three are RNA-Seq data from the Expression Atlas{target='_blank'}, while the last one is a microarray data set from GEO{target='_blank'}. Second, gene context analysis tools are introduced, which facilitate the visualization of gene modules sharing similar expression patterns. This includes the visualization of hierarchical clustering results with traditional matrix heatmaps (Matrix Heatmap) as well as co-expression network plots (Network). Third, the Spatial Enrichment functionality is illustrated with mouse RNA-seq data. Lastly, an overview of the corresponding Shiny App is presented that provides access to the same functionalities as the R functions, but executes them in an interactive GUI environment [@shiny; @shinydashboard].

Getting Started

Installation

The spatialHeatmap package should be installed from an R (version $\ge$ 3.6) session with the BiocManager::install command.

```{ eval=FALSE, echo=TRUE, warnings=FALSE} if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("spatialHeatmap")

## Packages and Documentation

Next, the packages required for running the sample code in this vignette need to be loaded.  

```r
library(spatialHeatmap); library(SummarizedExperiment); library(ExpressionAtlas); library(GEOquery); library(igraph); library(BiocParallel); library(kableExtra); library(org.Hs.eg.db); library(org.Mm.eg.db); library(ggplot2)

The following lists the vignette(s) of this package in an HTML browser. Clicking the corresponding name will open this vignette.

browseVignettes('spatialHeatmap')

To reduce runtime, intermediate results can be cached under ~/.cache/shm.

cache.pa <- '~/.cache/shm' # Path of the cache directory.

A temporary directory is created to save output files.

tmp.dir <- normalizePath(tempdir(check=TRUE), winslash="/", mustWork=FALSE)

Spatial Heatmaps {#shm}

Quick Start {#test}

Spatial Heatmaps (SHMs) are plotted with the shm function. To provide a quick and intuitive overview how these plots are generated, the following uses a generalized tesing example where a small vector of random numeric values is generated that are used to color features in an aSVG image. The image chosen for this example is an aSVG depicting the human brain. The corresponding image file homo_sapiens.brain.svg is included in this package for testing purposes.

aSVG Image

After the full path to the chosen target aSVG image on a user's system is obtained with the system.file function, the function read_svg is used to import the aSVG information relevant for creating SHMs, which is stored in an SVG object svg.hum.

svg.hum.pa <- system.file("extdata/shinyApp/data", 'homo_sapiens.brain.svg', package="spatialHeatmap")
svg.hum <- read_svg(svg.hum.pa)

All features and their attributes can be accessed with the attribute function, where fill and stroke are the two most important ones providing color and line width information, respectively. The feature column includes group labels for sub-features in the sub.feature column. SHM plots are created by mapping assay data to labels in feature.

feature.hum <- attribute(svg.hum)[[1]]
tail(feature.hum[, 1:6], 3) # Partial features and respective attributes

Feature coordinates can be accessed with the coordinate function.

coord.df <- coordinate(svg.hum)[[1]]
tail(coord.df, 3) # Partial features and respective coordinates

Numeric Data

The following generates a small named vector for testing, where the data slot contains four numbers, and the name slot is populated with three feature names and one missing one (here 'notMapped"). The numbers are mapped to features (feature.hum) via matching names among the numeric vector and the aSVG, respectively. Accordingly, only numbers and features with matching name counterparts can be colored in the aSVG image. In addition, a summary of the numeric assay to feature mappings is stored in a data.frame returned by the shm function (see below).

set.seed(20) # To obtain reproducible results, a fixed seed is set.
unique(feature.hum$feature)[1:10]
my_vec <- setNames(sample(1:100, 4), c('substantia.nigra', 'putamen', 'prefrontal.cortex', 'notMapped'))
my_vec

Plot SHM

Before plotting SHMs, the aSVG instance and numeric data are stored in an SPHM object for the sake of efficient data management and reusability.

dat.quick <- SPHM(svg=svg.hum, bulk=my_vec)

Next, the SHM is plotted with the shm function (Figure \@ref(fig:testshm)). Internally, the numbers in my_vec are translated into colors based on the color key and then painted onto the corresponding features in the aSVG. In the given example (Figure \@ref(fig:testshm)) only three features ('substantia.nigra', 'putamen', and 'prefrontal.cortex') in the aSVG have matching entries in the data my_vec.

shm.res <- shm(data=dat.quick, ID='testing', ncol=1, sub.title.size=20, legend.nrow=3)

The named numeric values in my_vec, that have name matches with the features in the chosen aSVG, are stored in the mapped_feature slot.

# Mapped features
spatialHeatmap::output(shm.res)$mapped_feature

Human Brain {#hum}

This subsection introduces how to query and download cell- and tissue-specific assay data in the Expression Atlas database using the ExpressionAtlas package [@ebi]. After the choosen data is downloaded directly into a user\'s R session, the expression values for selected genes can be plotted onto a chosen aSVG image with or without prior preprocessing steps (e.g. normalization).

Gene Expression Data

The following example searches the Expression Atlas for expression data derived from specific tissues and species of interest, here 'cerebellum' and 'Homo sapiens', respectively.

all.hum <- read_cache(cache.pa, 'all.hum') # Retrieve data from cache.
if (is.null(all.hum)) { # Save downloaded data to cache if it is not cached.
  all.hum <- searchAtlasExperiments(properties="cerebellum", species="Homo sapiens")
  save_cache(dir=cache.pa, overwrite=TRUE, all.hum)
}

The search result contains r nrow(all.hum) accessions. In the following code, the accession 'E-GEOD-67196{target="blank"}' from Prudencio _et al. [-@Prudencio2015-wd] has been chosen, which corresponds to an RNA-Seq profiling experiment of 'cerebellum' and 'frontal cortex' brain tissue from patients with amyotrophic lateral sclerosis (ALS).

all.hum[2, ]

The getAtlasData function allows to download the chosen RNA-Seq experiment from the Expression Atlas and import it into a RangedSummarizedExperiment object.

rse.hum <- read_cache(cache.pa, 'rse.hum') # Read data from cache.
if (is.null(rse.hum)) { # Save downloaded data to cache if it is not cached.
  rse.hum <- getAtlasData('E-GEOD-67196')[[1]][[1]]
  save_cache(dir=cache.pa, overwrite=TRUE, rse.hum)
}

The design of the downloaded RNA-Seq experiment is described in the colData slot of rse.hum. The following returns only its first four rows and columns.

colData(rse.hum)[1:2, c(2, 4)]

aSVG Image {#humSVG}

The following example shows how to download from the above described SVG repositories an aSVG image that matches the tissues and species assayed in the gene expression data set downloaded above. The return_feature function queries the repository for feature- and species-related keywords, here c('frontal cortex', 'cerebellum') and c('homo sapiens', 'brain'), respectively.

The remote data are downloaded before calling return_feature.

# Remote aSVG repos.
data(aSVG.remote.repo)
tmp.dir.ebi <- file.path(tmp.dir, 'ebi.zip')
tmp.dir.shm <- file.path(tmp.dir, 'shm.zip')
# Download the remote aSVG repos as zip files.
download.file(aSVG.remote.repo$ebi, tmp.dir.ebi)
download.file(aSVG.remote.repo$shm, tmp.dir.shm)
remote <- list(tmp.dir.ebi, tmp.dir.shm)

The downloaded aSVG repos are queried and returned aSVG files are saved in an empty directory (tmp.dir) to avoid overwriting of existing SVG files.

tmp.dir <- file.path(tempdir(check=TRUE), 'shm') # Empty directory. 
feature.df.hum <- return_feature(feature=c('frontal cortex', 'cerebellum'), species=c('homo sapiens', 'brain'), dir=tmp.dir, remote=remote) # Query aSVGs
feature.df.hum[1:8, ] # Return first 8 rows for checking
unique(feature.df.hum$SVG) # Return all matching aSVGs

To build this vignettes according to Bioconductor's package requirements, the following code section uses aSVG file instances included in the spatialHeatmap package rather than the downloaded instances above.

svg.dir <- system.file("extdata/shinyApp/data", package="spatialHeatmap") # Directory of the aSVG collection in spatialHeatmap
feature.df.hum <- return_feature(feature=c('frontal cortex', 'cerebellum'), species=c('homo sapiens', 'brain'), keywords.any=TRUE, return.all=FALSE, dir=svg.dir, remote=NULL)

Note, the target tissues frontal cortex and cerebellum are included in both the experimental design slot of the downloaded expression data as well as the annotations of the aSVG. This way these features can be colored in the downstream SHM plots. If necessary users can also change from within R the feature identifiers in an aSVG (see Supplementary Section).

tail(feature.df.hum[, c('feature', 'stroke', 'SVG')], 3)

Among the returned aSVG files, homo_sapiens.brain.svg is chosen for creating SHMs. Since it is the same as the Quick Start, the aSVG stored in svg.hum is used in the downstream steps.

Experimental Design

To display 'pretty' sample names in columns and legends of downstream tables and plots respectively, the following example imports a 'targets' file that can be customized by users in a text program. The targets file content is used to replace the text in the colData slot of the RangedSummarizedExperiment object with a version containing shorter sample names for plotting purposes.

The custom targets file is imported and then loaded into colData slot of rse.hum. A slice of the simplified colData object is shown below.

hum.tar <- system.file('extdata/shinyApp/data/target_human.txt', package='spatialHeatmap')
target.hum <- read.table(hum.tar, header=TRUE, row.names=1, sep='\t') # Importing
colData(rse.hum) <- DataFrame(target.hum) # Loading to "colData"
colData(rse.hum)[c(1:2, 41:42), 4:5]

Preprocess Assay Data

The raw count gene expression data is stored in the assay slot of rse.hum. The following shows how to apply basic preprocessing routines on the count data, such as normalizing, aggregating replicates, and removing genes with unreliable expression responses, which are optional for plotting SHMs.

The norm_data function is developed to normalize RNA-seq raw count data. The following example uses the ESF normalization option due to its good time performance, which is estimateSizeFactors from DESeq2 [@deseq2].

se.nor.hum <- norm_data(data=rse.hum, norm.fun='ESF', log2.trans=TRUE)

Replicates are aggregated with the summary statistics chosen under the aggr argument (e.g. aggr='mean'). The columns specifying replicates can be assigned to the sam.factor and con.factor arguments corresponding to samples and conditions, respectively. For tracking, the corresponding sample/condition labels are used as column titles in the aggregated assay instance, where they are concatenated with a double underscore as separator (Table \@ref(tab:humtab)).

se.aggr.hum <- aggr_rep(data=se.nor.hum, sam.factor='organism_part', con.factor='disease', aggr='mean')
assay(se.aggr.hum)[c(120, 49939, 49977), ]
cna <- c("cerebellum\\_\\_ALS", "frontal.cortex\\_\\_ALS", "cerebellum\\_\\_normal", "frontal.cortex\\_\\_normal")
kable(assay(se.aggr.hum)[c(120, 49939, 49977), ], caption='Slice of aggregated expression matrix.', col.names=cna, escape=TRUE, row.names=TRUE) %>% kable_styling("striped", full_width = FALSE) %>% scroll_box(width = "700px", height = "220px")

The filtering example below retains genes with expression values larger than 5 (log2 space) in at least 1% of all samples (pOA=c(0.01, 5)), and a coefficient of variance (CV) between 0.30 and 100 (CV=c(0.30, 100)). After that, the Ensembl gene ids are converted to UniProt ids with the function cvt_id.

se.fil.hum <- filter_data(data=se.aggr.hum, sam.factor='organism_part', con.factor='disease', pOA=c(0.01, 5), CV=c(0.3, 100))
se.fil.hum <- cvt_id(db='org.Hs.eg.db', data=se.fil.hum, from.id='ENSEMBL', to.id='SYMBOL')

SHM: Multiple Genes

Spatial features of interest can be subsetted with the function sub_sf by assigning their indexes (see below) to the argument show. In the following, 'brain outline', 'prefrontal.cortex', 'frontal.cortex', and 'cerebellum' are subsetted.

Next, for efficient data management and reusability the subset aSVG and assay data are stored in an SPHM object.

# Subsetting aSVG features.
svg.hum.sub <- sub_sf(svg.hum, show=c(64:132, 162:163, 164, 190:218))
tail(attribute(svg.hum.sub)[[1]][, 1:6], 3)
# Storing assay data and subsetted aSVG in an 'SPHM' object.
dat.hum <- SPHM(svg=svg.hum.sub, bulk=se.fil.hum)

SHMs for multiple genes can be plotted by providing the corresponding gene IDs under the ID argument as a character vector. The shm function will then sequentially arrange the SHMs for each gene in a single composite plot. To facilitate comparisons among expression values across genes and/or conditions, the lay.shm parameter can be assigned gene or con, respectively. For instance, in Figure \@ref(fig:mul) the SHMs of the genes OLFM4 and PRSS22 are organized by condition in a horizontal view. This functionality is particularly useful when comparing associated genes such as gene families.

res.hum <- shm(data=dat.hum, ID=c('OLFM4', 'PRSS22'), lay.shm='con', legend.r=1.5, legend.nrow=3, h=0.6)

In the above example, the normalized expression values of chosen genes are used to color the frontal cortex and cerebellum, where the different conditions, here normal and ALS, are given in separate SHMs. The color and feature mappings are defined by the corresponding color key and legend plot on the left and right, respectively.

By default, spatial features in assay data are mapped to their counterparts in aSVG according to the same identifiers on a one-to-one basis. However, the mapping can be customized, such as mapping a spatial feature in the data to a different or multiple counterparts in the aSVG. This advanced functionality is demonstrated in the Supplementary Section.

SHM: Other Selected Features

SHMs can be saved to interactive HTML files as well as video files. Each HTML file contains an interactive SHM with zooming in and out functionality. Hovering over graphics features will display data, gene, condition and other information. The video will play the SHM subplots in the order specified under the lay.shm argument.

The following example saves the interactive HTML and video files under the directory tmp.dir.

shm(data=dat.hum, ID=c('OLFM4', 'PRSS22'), lay.shm='con', legend.r=1.5, legend.nrow=3, h=0.6, aspr=2.3, animation.scale=0.7, bar.width=0.1, bar.value.size=4, out.dir=tmp.dir)

The following code saves individual SHMs into the same SVG file shm_hum.svg with the color scale and legend plot included.

res <- shm(data=dat.hum, ID=c('OLFM4', 'PRSS22'), lay.shm='con', legend.r=1.5, legend.nrow=3, h=0.5, aspr=2.3, animation.scale=0.7, bar.width=0.08, bar.value.size=12)
ggsave(file="./shm_hum.svg", plot=output(res)$spatial_heatmap, width=10, height=8) 

The following code exports each SHM (associated with a specific gene and condition) as separate SVG files in tmp.dir. In contrast to the original aSVG file, spatial features in the output SVG files are assigned heat colors.

write_svg(input=res, out.dir=tmp.dir)

A meta function plot_meta is developed as a wraper of individual steps necessary for plotting SHMs. The benefit of this function is creating SHMs with the Linux command line as shown below.

Rscript -e "spatialHeatmap::plot_meta(svg.path=system.file('extdata/shinyApp/data', 'mus_musculus.brain.svg', package='spatialHeatmap'), bulk=system.file('extdata/shinyApp/data', 'bulk_mouse_cocluster.rds', package='spatialHeatmap'), sam.factor='tissue', aggr='mean', ID=c('AI593442', 'Adora1'), ncol=1, bar.width=0.1, legend.nrow=5, h=0.6)"

SHM: Customization

To provide a high level of flexibility, many arguments are developed for shm. An overview of important arguments and their utility is provided in Table \@ref(tab:arg).

arg.df <- read.table('file/spatial_hm_arg.txt', header=TRUE, row.names=1, sep='\t')
kable(arg.df, caption='List of important argumnets of \'shm\'.', col.names=colnames(arg.df), row.names=TRUE, escape=TRUE) %>% kable_styling("striped", full_width = FALSE) %>% scroll_box(width = "650px", height = "230px")  

Mouse Organs {#mus}

This section generates an SHM plot for mouse data from the Expression Atlas. The code components are very similar to the previous Human Brain example. For brevity, the corresponding text explaining the code has been reduced to a minimum.

Gene Expression Data

The chosen mouse RNA-Seq data compares tissue level gene expression across mammalian species [@Merkin2012-ak]. The following searches the Expression Atlas for expression data from 'kidney' and 'Mus musculus'.

all.mus <- read_cache(cache.pa, 'all.mus') # Retrieve data from cache.
if (is.null(all.mus)) { # Save downloaded data to cache if it is not cached.
  all.mus <- searchAtlasExperiments(properties="kidney", species="Mus musculus")
  save_cache(dir=cache.pa, overwrite=TRUE, all.mus)
}

Among the many matching entries, accession 'E-MTAB-2801' will be downloaded.

all.mus[7, ]
rse.mus <- read_cache(cache.pa, 'rse.mus') # Read data from cache.
if (is.null(rse.mus)) { # Save downloaded data to cache if it is not cached.
  rse.mus <- getAtlasData('E-MTAB-2801')[[1]][[1]]
  save_cache(dir=cache.pa, overwrite=TRUE, rse.mus)
}

The design of the downloaded RNA-Seq experiment is described in the colData slot of rse.mus. The following returns only its first three rows.

colData(rse.mus)[1:3, ]

aSVG Image

The following example shows how to retrieve from the remote SVG repositories an aSVG image that matches the tissues and species assayed in the downloaded data above. The sample data from Human Brain are used such as remote.

feature.df.mus <- return_feature(feature=c('heart', 'kidney'), species=c('Mus musculus'), dir=tmp.dir, remote=remote)

To meet the R/Bioconductor package requirements, the following uses aSVG file instances included in the spatialHeatmap package rather than the downloaded instances.

feature.df.mus <- return_feature(feature=c('heart', 'kidney'), species=NULL, dir=svg.dir, remote=NULL) 

Return the names of the matching aSVG files.

unique(feature.df.mus$SVG)

The mus_musculus.male.svg instance is selected and imported.

svg.mus.pa <- system.file("extdata/shinyApp/data", "mus_musculus.male.svg", package="spatialHeatmap")
svg.mus <- read_svg(svg.mus.pa)

Experimental Design

A sample target file that is included in this package is imported and then loaded to the colData slot of rse.mus. To inspect its content, the first three rows are shown.

mus.tar <- system.file('extdata/shinyApp/data/target_mouse.txt', package='spatialHeatmap')
target.mus <- read.table(mus.tar, header=TRUE, row.names=1, sep='\t') # Importing
colData(rse.mus) <- DataFrame(target.mus) # Loading
target.mus[1:3, ]

Preprocess Assay Data

The raw RNA-Seq counts are preprocessed with the following steps: (1) normalization, (2) aggregation of replicates, and (3) filtering of un-reliable expression data. The details of these steps are explained in the sub-section of the Human Brain example.

rse.mus <- cvt_id(db='org.Mm.eg.db', data=rse.mus, from.id='ENSEMBL', to.id='SYMBOL', desc=TRUE) # Convert Ensembl ids to UniProt ids.  
se.nor.mus <- norm_data(data=rse.mus, norm.fun='CNF', log2.trans=TRUE) # Normalization
se.aggr.mus <- aggr_rep(data=se.nor.mus, sam.factor='organism_part', con.factor='strain', aggr='mean') # Aggregation of replicates
se.fil.mus <- filter_data(data=se.aggr.mus, sam.factor='organism_part', con.factor='strain', pOA=c(0.01, 5), CV=c(0.6, 100)) # Filtering of genes with low counts and variance 

SHM: Transparency

The pre-processed expression data for gene Scml2 is plotted in form of an SHM. In this case the plot includes expression data for 8 tissues across 3 mouse strains.

dat.mus <- SPHM(svg=svg.mus, bulk=se.fil.mus)
shm(data=dat.mus, ID=c('H19'), legend.width=0.7, legend.text.size=10, sub.title.size=9, ncol=3, ft.trans=c('skeletal muscle'), legend.ncol=2, line.size=0.2, line.color='grey70')

The SHM plots in Figures \@ref(fig:musshm) and below demonstrate the usage of the transparency feature via the ft.trans parameter. The corresponding mouse organ aSVG image includes overlapping tissue layers. In this case the skelectal muscle layer partially overlaps with lung and heart tissues. To view lung and heart in Figure \@ref(fig:musshm), the skelectal muscle tissue is set transparent with ft.trans=c('skeletal muscle').

To fine control the visual effects in feature rich aSVGs, the line.size and line.color parameters are useful. This way one can adjust the thickness and color of complex structures.

gg <- shm(data=dat.mus, ID=c('H19'), legend.text.size=10, sub.title.size=9, ncol=3, legend.ncol=2, line.size=0.1, line.color='grey70')

A third example on real data from Expression Atlas is SHMs of time series across chicken organs. Since the procedures are the same with the examples above, this example is illustrated in the Supplementary Section.

Arabidopsis Shoot {#shoot}

This section generates an SHM for Arabidopsis thaliana tissues with gene expression data from the Affymetrix microarray technology. The chosen experiment used ribosome-associated mRNAs from several cell populations of shoots and roots that were exposed to hypoxia stress [@Mustroph2009-nu]. In this case the expression data will be downloaded from GEO{target="_blank"} with utilites from the GEOquery package [@geo]. The data preprocessing routines are specific to the Affymetrix technology. The remaining code components for generating SHMs are very similar to the previous examples. For brevity, the text in this section explains mainly the steps that are specific to this data set.

Gene Expression Data

The GSE14502 data set is downloaded with the getGEO function from the GEOquery package. Intermediately, the expression data is stored in an ExpressionSet container [@biobase], and then converted to a SummarizedExperiment object.

gset <- read_cache(cache.pa, 'gset') # Retrieve data from cache.
if (is.null(gset)) { # Save downloaded data to cache if it is not cached.
  gset <- getGEO("GSE14502", GSEMatrix=TRUE, getGPL=TRUE)[[1]]
  save_cache(dir=cache.pa, overwrite=TRUE, gset)
}
se.sh <- as(gset, "SummarizedExperiment")

The gene symbol identifiers are extracted from the rowData component to be used as row names. Similarly, one can work with AGI identifiers by providing below AGI under Gene.Symbol.

rownames(se.sh) <- make.names(rowData(se.sh)[, 'Gene.Symbol'])

A slice of the experimental design stored in the colData slot is returned. Both the samples and treatments are contained in the title column. The samples are indicated by corresponding promoters (pGL2, pCO2, pSCR, pWOL, p35S) and treatments include control and hypoxia.

colData(se.sh)[60:63, 1:2]

aSVG Image

In this example, the aSVG image has been generated in Inkscape from the corresponding figure in @Mustroph2009-nu. Detailed instructions for generating custom aSVG images are provided in the SVG tutorial{target="_blank"}. The resulting custom aSVG file 'arabidopsis.thaliana_shoot_shm.svg' is included in the spatialHeatmap package and imported as below.

svg.sh.pa <- system.file("extdata/shinyApp/data", "arabidopsis.thaliana_shoot_shm.svg", package="spatialHeatmap")
svg.sh <- read_svg(svg.sh.pa)

Experimental Design

A sample target file that is included in this package is imported and then loaded to the colData slot of se.sh. To inspect its content, four selected rows are returned.

sh.tar <- system.file('extdata/shinyApp/data/target_arab.txt', package='spatialHeatmap')
target.sh <- read.table(sh.tar, header=TRUE, row.names=1, sep='\t') # Importing
colData(se.sh) <- DataFrame(target.sh) # Loading
target.sh[60:63, ]

Preprocess Assay Data

The downloaded GSE14502 data set has already been normalized with the RMA algorithm [@affy]. Thus, the pre-processing steps can be restricted to replicate aggregation and filtering.

se.aggr.sh <- aggr_rep(data=se.sh, sam.factor='samples', con.factor='conditions', aggr='mean') # Replicate agggregation using mean
se.fil.arab <- filter_data(data=se.aggr.sh, sam.factor='samples', con.factor='conditions', pOA=c(0.03, 6), CV=c(0.30, 100)) # Filtering of genes with low intensities and variance

SHM: Microarray

The expression profile for the HRE2 gene is plotted for the control and the hypoxia treatment across six cell types (Figure \@ref(fig:shshm)).

dat.sh <- SPHM(svg=svg.sh, bulk=se.fil.arab)
shm(data=dat.sh, ID=c("HRE2"), legend.ncol=2, legend.text.size=10, legend.key.size=0.02)

Superimposing raster and vector graphics

spatialHeatmap allows to superimpose raster images with vector-based SHMs. This way one can generate SHMs that resemble photographic representations of tissues, organs or entire organisms. For this to work the shapes represented in the vector-graphics need to be an aligned carbon copy of the raster image. Supported file formats for the raster image are JPG/JPEG and PNG, and for the vector image it is SVG. Matching raster and vector graphics are indicated by identical base names in their file names (e.g. imageA.png and imageA.svg). The layout order in SHMs composed of multiple independent images can be controlled by numbering the corresponding file pairs accordingly such as imageA_1.png and imageA_1.svg, imageA_2.png and imageA_2.svg, etc.

In the following example, the required image pairs have been pre-generated from a study on abaxial bundle sheath (ABS) cells in maize leaves [@Bezrutczyk2021-fq]. Their file names are labeled 1 and 2 to indicate two developmental stages.

Import paths of first png/svg image pair:

raster.pa1 <- system.file('extdata/shinyApp/data/maize_leaf_shm1.png', package='spatialHeatmap')
svg.pa1 <- system.file('extdata/shinyApp/data/maize_leaf_shm1.svg', package='spatialHeatmap')

Import paths of second png/svg image pair:

raster.pa2 <- system.file('extdata/shinyApp/data/maize_leaf_shm2.png', package='spatialHeatmap')
svg.pa2 <- system.file('extdata/shinyApp/data/maize_leaf_shm2.svg', package='spatialHeatmap')

The two pairs of png/svg images are imported in the SVG container svg.overlay.

svg.overlay <- read_svg(svg.path=c(svg.pa1, svg.pa2), raster.path=c(raster.pa1, raster.pa2))

A slice of attributes in the first aSVG instance is shown.

attribute(svg.overlay)[[1]][1:3, ]

Create random quantitative assay data.

df.ovl <- data.frame(matrix(runif(6, min=0, max=5), nrow=3))
colnames(df.ovl) <- c('cell1', 'cell2') # Assign column names.
rownames(df.ovl) <- paste0('gene', seq_len(3)) # Assign row names 
df.ovl[1:2, ]

To minimize masking of the features in the SHMs by dense regions in the raster images, the alpha.overlay argument allows to adjust the transparency level. In Figure \@ref(fig:overCol), the spatial features of interest are superimposed onto the raster image.

dat.over <- SPHM(svg=svg.overlay, bulk=df.ovl)
shm(data=dat.over, charcoal=FALSE, ID=c('gene1'), alpha.overlay=0.5, bar.width=0.09, sub.title.vjust=4, legend.r=0.2)

Another option for reducing masking effects is to display the raster image in black and white by setting charcoal=TRUE (Figure \@ref(fig:overChar)).

shm(data=dat.over, charcoal=TRUE, ID=c('gene1'), alpha.overlay=0.5, bar.width=0.09, sub.title.vjust=4, legend.r=0.2)

SHMs of Multiple Variables {#sthm}

The SHM plots shown so far are restricted to two variables, here spatial features (e.g. tissues) and treatments. In theory, the complexity of experimental designs scales to any number of variables in spatialHeatmap. This section extends to experiments with three or more variables, such as experiments with spatiotemporal resolution and geographical locations, genotypes, treatments, etc.

To visualize multi-variable assay data, the variables are reduced to two by keeping the spatial feature unchanged and combining all other variables into a composite one. For instance, the following example contains four variables including spatial features, time points, drug treatments and injury conditions. The latter three are combined to produce a composite variable.

Gene Expression Data

The following uses RNA-seq data assayed from hippocampus and hypothalamus in mouse brain, and the experimental variables include traumatic brain injury (TBI), 3 or 29 days post injury (DPI), candesartan or vehicle treatment [@Attilio2021-pp]. The original data are modified for demonstration purpose and included in spatialHeatmap as a SummarizedExperiment object, which is imported below.

se.mus.vars <- readRDS(system.file('extdata/shinyApp/data/mus_brain_vars_se.rds', package='spatialHeatmap'))

The experiment design is stored in colData slot, where 'Veh', 'Drug', 'TBI', and 'NoTBI' refer to 'vehicle', 'candesartan', 'traumatic brain injury', and 'sham injury' respectively. The time, treatment and injury variables are combined into a composite one comVar.

colData(se.mus.vars)[1:3, ]
unique(colData(se.mus.vars)$comVar)

Since this example data are small, the pre-processing only involves normalization without the filtering step. The expression values are aggregated across replicates in tissues (tissue) and replicates in the composite variable (comVar) with the summary statistic of mean, which is similar with the Human Brain exmple.

se.mus.vars.nor <- norm_data(data=se.mus.vars, norm.fun='ESF', log2.trans=TRUE) # Normalization.
se.mus.vars.aggr <- aggr_rep(data=se.mus.vars.nor, sam.factor='tissue', con.factor='comVar', aggr='mean') # Aggregate replicates.
assay(se.mus.vars.aggr)[1:3, 1:3]

aSVG Image

The aSVG image of mouse brain is downloaded from the [EBI anatomogram] repository (https://github.com/ebi-gene-expression-group/anatomogram/tree/master/src/svg){target="_blank"} and included in spatialHeatmap, which is imported as below.

svg.mus.brain.pa <- system.file("extdata/shinyApp/data", "mus_musculus.brain.svg", package="spatialHeatmap")
svg.mus.brain <- read_svg(svg.mus.brain.pa)

The aSVG features and attributes are partially shown.

tail(attribute(svg.mus.brain)[[1]], 3)

SHM: Multiple Variables

The expression values of gene Acnat1 in hippocampus and hypothalamus across the composite variable are mapped to matching aSVG features. The output SHM plots of each composite variable are organized in a composite plot in Figure \@ref(fig:dimshm).

dat.mul.dim <- SPHM(svg=svg.mus.brain, bulk=se.mus.vars.aggr)
shm(data=dat.mul.dim, ID=c('Acnat1'), legend.r=1.5, legend.key.size=0.02, legend.text.size=12, legend.nrow=3)

Multiple aSVGs {#mul_svg}

In a spatiotemporal application, different development stages may need to be represented in separate aSVG images. In such a case, the shm function is able to arrange multiple aSVGs in a single SHM plot. To organize the subplots, the names of the separate aSVG files are expected to include the following suffixes: *_shm1.svg, *_shm2.svg, etc.
As a simple testing example, the following stores random numbers as expression values in a data.frame.

df.random <- data.frame(matrix(runif(50, min=0, max=10), nrow=10))
colnames(df.random) <- c('shoot_totalA__treatment1', 'shoot_totalA__treatment2', 'shoot_totalB__treatment1', 'shoot_totalB__treatment2', 'notMapped') # Assign column names
rownames(df.random) <- paste0('gene', 1:10) # Assign row names 
df.random[1:2, ]

The paths to the aSVG files are obtained, here for younger and older plants using *_shm1 and *_shm1, respectively, which are generated from @Mustroph2009-nu. Subsequently, the two aSVG files are loaded with the read_svg function.

svg.sh1 <- system.file("extdata/shinyApp/data", "arabidopsis.thaliana_organ_shm1.svg", package="spatialHeatmap")
svg.sh2 <- system.file("extdata/shinyApp/data", "arabidopsis.thaliana_organ_shm2.svg", package="spatialHeatmap")
svg.sh.mul <- read_svg(c(svg.sh1, svg.sh2))

The following generates the corresponding SHMs plot for gene2. The orginal image dimensions can be preserved by assigning TRUE to the preserve.scale argument.

dat.mul.svg <- SPHM(svg=svg.sh.mul, bulk=df.random)
shm(data=dat.mul.svg, ID=c('gene2'), width=0.7, legend.r=0.2, legend.width=1, preserve.scale=TRUE, bar.width=0.09, line.color='grey50') 

Note in Figure \@ref(fig:arabshm) shoots are drawn with thicker outlines than roots. This is another useful feature of shm, i.e. preserving the outline thicknesses defined in aSVG files. This feature is particularly useful in cellular SHMs where different cell types may have different cell-wall thicknesses. The outline widths can be updated with update_feature programatically, or within Inkscape manually. The former is illustrated in the Supplementary Section.

Extended functionalities

Spatial Enrichment {#se}

The Spatial Enrichment (SpEn) functionality is an extension of SHMs for identifying groups of biomolecules (e.g. RNAs, proteins, metabolites) that are particularly abundant or enriched in certain spatial regions, such as tissue-specific transcripts. Given a group of spatial features, SpEn identifies biomolecules significantly up- or down-regulated in each spatial feature relative to all other features (references). These biomolecules are classified as spatially enriched or depleted respectively. Then by querying a feature in the enrichment results, the corresponding enriched and depleted biomolecules will be returned, and their abundance values are subsequently visualized as enrichment SHMs. Similarly, biomolecules enriched or depleted in one experimental variable relative to reference variables can be detected and visualized as well. SpEn utilizes differential expression (DE) analysis methods to detect enriched or depleted biomolecules, including edgeR [@edgeR], limma [@limma], DESeq2 [@deseq2].

The application of SpEn is illustrated with the above mouse organ data. The function sf_var is used to subset spatial features and experiment variables of interest in the assay data. In the following, five features ('brain', 'liver', 'lung', 'colon', and 'kidney') and three experiment variables (mouse strains 'DBA.2J', 'C57BL.6', and 'CD1') are subsetted. The com.by argument specifies whether the enrichment will be performed on spatial features (ft) or variables (var). In the following, com.by is set ft, so SpEn is performed for spatial features and the variables under each spatial feature are treated as replicates.

sub.mus <- sf_var(data=rse.mus, feature='organism_part', ft.sel=c('brain', 'lung', 'colon', 'kidney', 'liver'), variable='strain', var.sel=c('DBA.2J', 'C57BL.6', 'CD1'), com.by='ft')
colData(sub.mus)[1:3, c('organism_part', 'strain')]

The subsetted data are filtered. Details about this step are given under the human brain section.

sub.mus.fil <- filter_data(data=sub.mus, pOA=c(0.5, 15), CV=c(0.8, 100), verbose=FALSE)

The SpEn is implemented in the function spatial_enrich. In the following, the method edgeR is chosen and the count data are internally normalized by the TMM method from edgeR. The enrichment results are selected by log2 fold change (log2.fc) and FDR (fdr). The outliers argument specifies a number of outliers allowed in references.

enr.res <- spatial_enrich(sub.mus.fil, method=c('edgeR'), norm='TMM', log2.fc=1, fdr=0.05, outliers=1)

The overlap of enriched biomolecules (type='up') across spatial features are presented in an UpSet plot (plot='upset'). Assigning matrix or venn to the plot argument will present the overlaps in form of a matrix plot or Venn diagram respectively.

ovl_enrich(enr.res, type='up', plot='upset')

The enriched and depleted genes in brain are queried with the function query_enrich. In the type column, 'up' and 'down' refer to 'enriched' and 'depleted' respectively, while the total column shows the total reference features excluding outliers.

en.brain <- query_enrich(enr.res, 'brain')
up.brain <- subset(rowData(en.brain), type=='up' & total==4)
up.brain[1:2, 1:3] # Enriched.
dn.brain <- subset(rowData(en.brain), type=='down' & total==4)
dn.brain[1:2, 1:3] # Depleted. 

One enriched (Kif5c) and one depleted (Cdhr5) gene in mouse brain are chosen to plot SHMs. The resulting SHMs are termed as SHMs of spatially-enriched/depleted biomolecules (enrichment SHMs) respectively.

dat.enrich <- SPHM(svg=svg.mus, bulk=en.brain)
shm(data=dat.enrich, ID=c('Kif5c', 'Cdhr5'), legend.r=1, legend.nrow=7, sub.title.size=15, ncol=3, bar.width=0.09, lay.shm='gene')

The expression profiles of the two chosen genes (Figure \@ref(fig:enr)) are also presented in line graphs.

graph_line(assay(en.brain)[c('Kif5c', 'Cdhr5'), ], lgd.pos='right')

Hierarchical Clustering {#mhm}

SHMs are suitable for comparing assay profiles among small number of biomolecules (e.g. few genes or proteins) across cell types and conditions. To also support analysis routines of larger number of biomolecules, spatialHeatmap integrates functionalities for identifying groups of biomolecules with similar and/or dissimilar assay profiles, and subsequently analyzing the results with data mining methods that scale to larger numbers of biomolecules than SHMs, such as hierarchical clustering and network analysis methods.

To identify similar biomolecules, the submatrix function can be used. It identifies biomolecules sharing similar profiles with one or more query biomolecules of interest. The given example uses correlation coefficients as similarity metric. The p argument allows to restrict the number of similar biomolecules to return based on a percentage cutoff relative to the number of biomolecules in the assay data set (e.g. 1% of the top most similar biomolecules). If several query biomolecules are provided then the function returns the similar genes for each query, while assuring uniqueness among biomolecules in the result.

In a typical scenario, a spatial feature of interest is chosen in the first place, then a query biomolecule is chosen for the chosen feature, such as a tissue-specific gene. The following introduces the large-scale data mining using as sample data the preprocessed gene expression data (se.fil.mus) from the Mouse Organs section. The brain is selected as the query feature and 'Kif5c' is selected as the query gene, which is spatially enriched in brain and known to play important roles in motor neurons [@Kanai2000-tc].

sub.mat <- submatrix(data=se.fil.mus, ID='Kif5c', p=0.15)

The result from the previous step is the assay matrix subsetted to the genes sharing similar assay profiles with the query gene 'Kif5c'.

assay(sub.mat)[1:2, 1:3] # Subsetted assay matrix

Subsequently, hierarchical clustering is applied to the subsetted assay matrix containing only the genes that share profile similarities with the query gene 'Kif5c'. The clustering result is displayed as a matrix heatmap where the rows and columns are sorted by the corresponding hierarchical clustering dendrograms (Figure \@ref(fig:static)). The position of the query gene ('Kif5c') is indicated in the heatmap by black lines. Setting static=FALSE will launch the interactive mode, where users can zoom into the heatmap by selecting subsections in the image or zoom out by double clicking.

res.hc <- matrix_hm(ID=c('Kif5c'), data=sub.mat, angleCol=60, angleRow=60, cexRow=0.8, cexCol=0.8, margin=c(10, 6), static=TRUE, arg.lis1=list(offsetRow=0.01, offsetCol=0.01))

The most important information of Figure \@ref(fig:static) is returned in res.hc. The row dendrogram is saved in res.hc$rowDendrogram. By using the function cut_dendro, it can be cut at a certain height (here h=15) to obtain the cluster containing the query gene.

cut_dendro(res.hc$rowDendrogram, h=15, 'Kif5c')

Network Graphs {#net}

Module Identification

Network analysis is performed with the WGCNA algorithm [@Langfelder2008-sg; @Ravasz2002-db] using as input the subsetted assay matrix generated in the previous section. The objective is to identify network modules that can be visualized in the following step in form of network graphs. Applied to the gene expression sample data used here, these network modules represent groups of genes sharing highly similar expression profiles. Internally, the network module identification includes five major steps. First, a correlation matrix (Pearson or Spearman) is computed for each pair of biomolecules. Second, the obtained correlation matrix is transformed into an adjacency matrix that approximates the underlying global network to scale-free topology [@Ravasz2002-db]. Third, the adjacency matrix is used to calculate a topological overlap matrix (TOM) where shared neighborhood information among biomolecules is used to preserve robust connections, while removing spurious connections. Fourth, the distance transformed TOM is used for hierarchical clustering. To maximize time performance, the hierarchical clustering is performed with the flashClust package [@Langfelder2012-nv]. Fifth, network modules are identified with the dynamicTreeCut package [@dynamicTreeCut]. Its ds (deepSplit) argument can be assigned integer values from 0 to 3, where higher values increase the stringency of the module identification process. To simplify the network module identification process with WGCNA, the individual steps can be executed with a single function called adj_mod. The result is a list containing the adjacency matrix and the final module assignments stored in a data.frame. Since the interactive network feature used in the visualization step below performs best on smaller modules, only modules are returned that were obtained with stringent ds settings (here ds=2 and ds=3).

adj.mod <- adj_mod(data=sub.mat)

A slice of the adjacency matrix is shown below.

adj.mod[['adj']][1:3, 1:3]

The module assignments are stored in a data frame. Its columns contain the results for the ds=2 and ds=3 settings. Integer values $>0$ are the module labels, while $0$ indicates unassigned biomolecules. The following returns the first three rows of the module assignment result.

adj.mod[['mod']][1:3, ] 

Module Visualization

Network modules can be visualized with the network function. To plot a module containing a biomolecule (gene) of interest, its ID needs to be provided under the corresponding argument. Typically, this could be one of the biomolecules chosen for the above SHM plots. There are two modes to visualize the selected module: static or interactive. Figure \@ref(fig:inter) was generated with static=TRUE. Setting static=FALSE will generate the interactive version. In the network plot shown below the nodes and edges represent genes and their interactions, respectively. The thickness of the edges denotes the adjacency levels, while the size of the nodes indicates the degree of connectivity of each biomolecule in the network. The adjacency and connectivity levels are also indicated by colors (Figure \@ref(fig:inter)). The gene of interest assigned under ID is labeled in the plot with the suffix tag: *_target.

network(ID="Kif5c", data=sub.mat, adj.mod=adj.mod, adj.min=0, vertex.label.cex=1.2, vertex.cex=3, edge.cex=3, mar.key=c(3, 10, 1, 10), static=TRUE)

Setting static=FALSE launches the interactive network. In this mode there is an interactive color bar that denotes the gene connectivity. To modify it, the color labels need to be provided in a comma separated format, e.g.: yellow, orange, red. The latter would indicate that the gene connectivity increases from yellow to red.

If the expression matrix contains gene/protein annotation information in the rowData slot and specified through desc, then it will be shown when moving the cursor over a network node.

network(ID="Kif5c", data=sub.mat, adj.mod=adj.mod, desc='desc', static=FALSE)

Shiny App {#shiny}

In additon to running spatialHeatmap from R, the package includes a Shiny App{target="_blank"} that provides access to the same functionalities from an intuitive-to-use web browser interface. Apart from being very user-friendly, this App conveniently organizes the results of the entire visualization workflow in a single browser window with options to adjust the parameters of the individual components interactively. For instance, genes can be selected and replotted in SHMs simply by clicking the corresponding rows in the expression table included in the same window. This representation is very efficient in guiding the interpretation of the results in a visual and user-friendly manner. For testing purposes, the spatialHeatmap Shiny App also includes ready-to-use sample expression data and aSVG images along with embedded user instructions.

Local System

The Shiny App of spatialHeatmap can be launched from an R session with the following function call.

shiny_shm()

The main dashboard panels of the Shiny App are organized as follows:

  1. Datasets: options for uploading custom datasets, selecting default datsets, or downloading example datasets.
  2. Spatial Heatmap: interactive tables of assay data/metadata, plotting SHMs with single or multiple genes, settings to customize the SHMs.
  3. Spatial Enrichment: overlap plots of enrichment results across spatial features, data table of enriched and depleted biomolecules.
  4. Data Mining: hierarchical clustering, K-means clustering, network analysis.
  5. Co-visualization: co-visualizing single-cell and bulk data in embedding plots (PCA, UMAP, or TSNE) and SHMs repectively. This functionality is described in a separate vignette{target='_blank'}.

A screenshot is shown below depicting SHM plots generated with the spatialHeatmap Shiny App (Figure \@ref(fig:shiny)).

include_graphics('img/shiny.jpg')

The assay data along with metatdata are uploaded to the Shiny App as tabular (e.g. in CSV or TSV format) or '.rds' files. The latter is a SummarizedExperiment object saved with the saveRDS function. In addition, the images are uploaded as aSVG files. The filter_data function can be used to export assay data from SummarizedExperiment to tabular files (TSV format). In the following example, the file argument specifies the the output file name, while the sam.factor and con.factor specifies spatial features and experiment variables in the colData slot respectively, which will be retained in the column names of the output tabular file. An example of the output format is shown in Table \@ref(tab:humtab). In addition, the desc argument can be optionally used to specify gene annotations in the rowData slot, which will be appended to the output tabular file. More details of assay data formats are provided in the Supplement.

se.fil.arab <- filter_data(data=se.aggr.sh, desc="Target.Description", sam.factor='samples', con.factor='conditions', pOA=c(0.03, 6), CV=c(0.30, 100), file='./filtered_data.txt')

Server Deployment

As most Shiny Apps, spatialHeatmap can be deployed as a centralized web service. A major advantage of a web server deployment is that the functionalities can be accessed remotely by anyone on the internet without the need to use R on the user system. For deployment one can use custom web servers or cloud services, such as AWS, GCP or shinysapps.io{target="_blank"}. An example web instance for testing spatialHeatmap online is available here{target="_blank"}.

Custom Shiny App

The spatialHeatmap package also allows users to create custom Shiny App instances using the custom_shiny function. This function provides options to include custom assay and image data, and define default settings (e.g. color schemes). For details users want to consult the help file. To maximize flexibility, the default settings are stored in a yaml file in the App. This makes it easy to refine and optimize default settings simply by changing this yaml file.

Database Backend

To maintain scalability, the Shiny App is designed to work with backend databases that comprise assay datasets, aSVG files, and the pairing between assay data and aSVGs. This allows users to manage large amounts of assay data and aSVGs in a batch. Both SummarizedExperiment and SinleCellExperiment formats are supported data structures to create the backend database. Assay datasets are saved in the same HDF5 database [@rhdf5]. Then the assay data, aSVG files, and the pairing information (stored as a nested list) between assay data and aSVGs are compressed into a '.tar' file as the final database. More details are referred to the help file of write_hdf5.

Supplementary Section {#sup}

The advantages of integrating the features of spatialHeatmap are showcased in a discovery workflow{target='_blank'}.

Numeric Data {#data_form}

The numceric data used to color the features in aSVG images can be provided as three different object types including vector, data.frame and SummerizedExperiment. When working with complex omics-based assay data then the latter provides the most flexibility, and thus should be the preferred container class for managing numeric data in spatialHeatmap. Both data.frame and SummarizedExperiment can hold data from many measured biomolecules, such as many genes or proteins. In contrast to this, the vector class is only suitable for data from single biomolecules. Due to its simplicity this less complex container is often useful for testing or when dealing with simple data sets.

Object Types

vector

When using numeric vectors as input to shm, then their name slot needs to be populated with strings matching the feature names in the corresponding aSVG. To also specify experiment variables, their labels need to be appended to the feature names with double underscores as separator, i.e. 'spFfeature__variable'.

The following example replots the testing example for two spatial features ('putamen' and 'prefrontal.cortex') and two experiment variables ('1' and '2').

vec <- sample(x=1:100, size=5) # Random numeric values
names(vec) <- c('putamen__variable1', 'putamen__variable2', 'prefrontal.cortex__variable1', 'prefrontal.cortex__variable2', 'notMapped') # Assign unique names to random values
vec

With this configuration the resulting plot contains two SHMs for the human brain, corresponding to 'variable1' and 'variable2' respectively. To keep the build time of this package to a minimum, the shm function call in the code block below is not evaluated, and thus the corresponding SHMs are not shown.

dat.vec <- SPHM(svg=svg.hum, bulk=vec)
shm(data=dat.vec, ID='testing', ncol=1, legend.r=1.2, sub.title.size=14, ft.trans='g4320', legend.nrow=3)

data.frame {#df}

The data.frame stores assay data in a table, where columns and rows are spatial features/variables and biomolecules respectively. The naming of spatial features and variables in the column names follows the same convention as the above vector example. The following illustrates the data.frame container with random numbers.

df.test <- data.frame(matrix(sample(x=1:1000, size=100), nrow=20)) # Create numeric data.frame
colnames(df.test) <- names(vec) # Assign column names
rownames(df.test) <- paste0('gene', 1:20) # Assign row names
df.test[1:3, ]

With the resulting data.frame, SHMs can be plotted for one or multiple genes (ID=c('gene1')).

dat.df <- SPHM(svg=svg.hum, bulk=df.test)
shm(data=dat.df, ID=c('gene1'), ncol=1, legend.r=1.2, sub.title.size=14, legend.nrow=3)

Additional gene annotation information can be appended to the data.frame. This information can then be displayed interactively in the network plots of the Shiny App by placing the cursor over network nodes.

df.test$ann <- paste0('ann', 1:20)
df.test[1:3, ]

SummarizedExperiment

The SummarizedExperiment class is a much more extensible and flexible container for providing metadata for both rows and columns of numeric data.

To import experimental design information (e.g. replicates, treatments) from tabular files, users can provide a target file that will be stored in the colData slot of the SummarizedExperiment (SE) object. Usually, the target file contains at least two columns: one for spatial features and one for experimental variables, where replicates are indicated by identical entries. The actual numeric matrix representing the assay data is stored in the assay slot, where the rows correspond to biomolecules (e.g. genes). Optionally, additional annotation information for the rows (e.g. gene descriptions) can be stored in the rowData slot.

For constructing a valid SummarizedExperiment object that can be used by the shm function, the target file should meet the following requirements.

  1. It should contain at least two columns. One column represents spatial features (spFeature) and the other one experimental variables (variable) such as treatments. The rows in the target file correspond to the columns of the numeric data stored in the assay slot.

  2. To be colored in SHMs, the spatial features must have common identifiers between the assay data and aSVG. Note, the double underscore is a special string reserved for specific purposes in spatialHeatmap, and thus should be avoided for naming spatial features and variables.

The following example illustrates the design of a valid SummarizedExperiment object for generating SHMs. In this example, the 'putamen' tissue has 2 variables and each has 2 replicates. Thus, there are 4 assays for putamen. The same design applies to the prefrontal.cortex tissue.

spft <- c(rep('putamen', 4), rep('prefrontal.cortex', 4))
vars <- rep(c('variable1', 'variable1', 'variable2', 'variable2'), 2)
target.test <- data.frame(spFeature=spft, variable=vars, row.names=paste0('assay', 1:8))
target.test

The assay slot is populated with a data.frame containing random numbers. Each column corresponds to an assay in the target file (here imported into colData), while each row corresponds to a gene.

df.se <- data.frame(matrix(sample(x=1:1000, size=160), nrow=20))
rownames(df.se) <- paste0('gene', 1:20)
colnames(df.se) <- row.names(target.test)
df.se[1:3, ]

Next, the final SummarizedExperiment object is constructed by providing the numeric and target data under the assays and colData arguments, respectively.

se <- SummarizedExperiment(assays=df.se, colData=target.test)
se

In addition, row-wise annotation information (e.g. for genes) can be included in the rowData slot.

rowData(se) <- df.test['ann']

The replicates are aggregated by means.

se.aggr <- aggr_rep(data=se, sam.factor='spFeature', con.factor='variable', aggr='mean')
assay(se.aggr)[1:2, ]

With the fully configured SummarizedExperiment object, a similar SHM is plotted as in the previous examples.

dat.se <- SPHM(svg=svg.hum, bulk=se.aggr)
shm(data=dat.se, ID=c('gene1'), ncol=1, legend.r=1.2, sub.title.size=14, ft.trans=c('g4320'), legend.nrow=3)

aSVGs files

aSVG repositories {#svg_repo}

The aSVG files can be created by following our step-by-step tutorial{target="_blank"} or downloaded from public repositories. A public aSVG repository, that can be used by spatialHeatmap directly, is the EBI anatomogram{target="_blank"}. It contains annatomical aSVG images from different species. The same aSVG images are also used by the web service of the Expression Atlas project. Furthermore, the spatialHeatmap has its own repository called spatialHeatmap aSVG Repository{target="_blank"}, which stores custom aSVG files developed for this project (e.g. Figure \@ref(fig:shshm)). In the future, we will expand our repository with more aSVGs, and users are encouraged to contribute their own aSVGs to this repository, allowing them to share their creations with the community.

Update aSVG features {#update}

To edit spatial feature identifiers in aSVGs, the update_feature function can be used. The demonstration below first creates an empty folder tmp.dir1 and copies into it the aSVG homo_sapiens.brain.svg.

tmp.dir1 <- file.path(tempdir(check=TRUE), 'shm1') 
if (!dir.exists(tmp.dir1)) dir.create(tmp.dir1)
svg.hum.pa <- system.file("extdata/shinyApp/data", 'homo_sapiens.brain.svg', package="spatialHeatmap") 
file.copy(from=svg.hum.pa, to=tmp.dir1, overwrite=TRUE) # Copy "homo_sapiens.brain.svg" file into 'tmp.dir1'

The folder tmp.dir1 is queried with feature and species keywords, and matches are returned in a data.frame.

feature.df <- return_feature(feature=c('frontal cortex', 'prefrontal cortex'), species=c('homo sapiens', 'brain'), dir=tmp.dir1, remote=NULL, keywords.any=FALSE)
feature.df

New feature identifiers are stored in a vector, corresponding to each of the returned features (here 'prefrontal.cortex' and 'frontal.cortex').

f.new <- c('prefrontalCortex', 'frontalCortex')

To also update strokes (thickness of spatial feature outlines) and colors, store new strokes and colors in separate vectors in a similar way as above.

s.new <- c('0.05', '0.1') # New strokes.
c.new <- c('red', 'green') # New colors.

Next, new features, strokes, and colors are stored as three respective columns in a data.frame. The column names featureNew, strokeNew, and colorNew are internally recognized by the update_feature function when updating the aSVG.

feature.df.new <- cbind(featureNew=f.new, strokeNew=s.new, colorNew=c.new, feature.df)
feature.df.new

Finally, update_feature is used to update spatial features, strokes, and colors in the aSVG stored in the tmp.dir1 folder.

update_feature(df.new=feature.df.new, dir=tmp.dir1)

Advanced Functionalities

SHM: Re-matching {#remat}

spatialHeatmap supports re-matching one spatial feature in the assay data to one or multiple counterparts in the aSVG. The re-matching is defined in a named list. In the list, a name slot refers to a spatial feature in assay data and the corresponding list elements represent aSVG features for re-matching.

The example below takes assay data from the Human Brain section, such as svg.hum.sub and se.fil.hum. The spatial feature frontal.cortex in assay data is re-matched to frontal.cortex and prefrontal.cortex in the aSVG through a list (remat.hum). Figure \@ref(fig:shmNoMatch) is the SHM before re-matching while Figure \@ref(fig:remat) is the SHM after re-matching.

remat.hum <- list(frontal.cortex=c('frontal.cortex', 'prefrontal.cortex'))
dat.no.match <- SPHM(svg=svg.hum.sub, bulk=se.fil.hum)
shm(data=dat.no.match, ID=c('OLFM4'), lay.shm='con', ncol=1, legend.r=0.8, legend.nrow=2, h=0.6)
dat.rematch <- SPHM(svg=svg.hum.sub, bulk=se.fil.hum, match=remat.hum)
shm(data=dat.rematch, ID=c('OLFM4'), lay.shm='con', ncol=1, legend.r=0.8, legend.nrow=2, h=0.6)

Re-matching has various applications, such as mapping gene expression profiles from one species to a closely related species in the same anatomical region. It enables leveraging existing data when direct measurements are challenging. Additionally, re-matching can be used to map gene assay profiles of a sub-tissue to the whole tissue, when assaying the entire tissue is difficult. It allows extrapolating and analyzing gene expression patterns of the entire tissue based on data from the sub-tissues.

SHMs of Time Series {#chk}

This section generates a SHM plot for chicken data from the Expression Atlas. The code components are very similar to the Human Brain example. For brevity, the corresponding text explaining the code has been reduced to a minimum.

Gene Expression Data

The following searches the Expression Atlas for expression data from 'heart' and 'gallus'.

all.chk <- read_cache(cache.pa, 'all.chk') # Retrieve data from cache.
if (is.null(all.chk)) { # Save downloaded data to cache if it is not cached.
  all.chk <- searchAtlasExperiments(properties="heart", species="gallus")
  save_cache(dir=cache.pa, overwrite=TRUE, all.chk)
}

Among the matching entries, accession 'E-MTAB-6769' will be downloaded, which is an RNA-Seq experiment comparing the developmental changes across nine time points of seven organs [@Cardoso-Moreira2019-yq].

all.chk[3, ]
rse.chk <- read_cache(cache.pa, 'rse.chk') # Read data from cache.
if (is.null(rse.chk)) { # Save downloaded data to cache if it is not cached.
  rse.chk <- getAtlasData('E-MTAB-6769')[[1]][[1]]
  save_cache(dir=cache.pa, overwrite=TRUE, rse.chk)
}

The first three rows of the design in the downloaded experiment are shown.

colData(rse.chk)[1:3, ]

aSVG Image

The following example shows how to download from the above SVG repositories an aSVG image that matches the tissues and species assayed in the downloaded data. As before downloaded images are saved to the directory tmp.dir.

tmp.dir <- file.path(tempdir(check=TRUE), 'shm')
# Query aSVGs.
feature.df <- return_feature(feature=c('heart', 'kidney'), species=c('gallus'), dir=tmp.dir, remote=remote)

To meet the R/Bioconductor package requirements, the following uses aSVG file instances included in the spatialHeatmap package rather than the downloaded instances.

feature.df <- return_feature(feature=c('heart', 'kidney'), species=c('gallus'), dir=svg.dir, remote=NULL)
feature.df[1:2, c('feature', 'stroke', 'SVG')] # A slice of the search result.

The target aSVG instance gallus_gallus.svg is imported.

svg.chk.pa <- system.file("extdata/shinyApp/data", "gallus_gallus.svg", package="spatialHeatmap")
svg.chk <- read_svg(svg.chk.pa)

Experimental Design

A sample target file that is included in this package is imported and then loaded to the colData slot of rse.chk, the first three rows of which are displayed.

chk.tar <- system.file('extdata/shinyApp/data/target_chicken.txt', package='spatialHeatmap')
target.chk <- read.table(chk.tar, header=TRUE, row.names=1, sep='\t') # Importing
colData(rse.chk) <- DataFrame(target.chk) # Loading
target.chk[1:3, ]

Preprocess Assay Data

The raw RNA-Seq count are preprocessed with the following steps: (1) normalization, (2) aggregation of replicates, and (3) filtering of reliable expression data, details of which are seen in the Human Brain example.

se.nor.chk <- norm_data(data=rse.chk, norm.fun='ESF', log2.trans=TRUE) # Normalization
se.aggr.chk <- aggr_rep(data=se.nor.chk, sam.factor='organism_part', con.factor='age', aggr='mean') # Replicate agggregation using mean 
se.fil.chk <- filter_data(data=se.aggr.chk, sam.factor='organism_part', con.factor='age', pOA=c(0.01, 5), CV=c(0.6, 100)) # Filtering of genes with low counts and varince

SHM: Time Series

The expression profile for gene ENSGALG00000006346 is plotted across nine time points in four organs in form of a composite SHM with 9 panels. Their layout in three columns is controlled with the argument setting ncol=3. In the legend plot, spatial features are labeled by label=TRUE.

dat.chk <- SPHM(svg=svg.chk, bulk=se.fil.chk)
shm(data=dat.chk, ID='ENSGALG00000006346', width=0.9, legend.width=0.9, legend.r=1.5, sub.title.size=9, ncol=3, legend.nrow=3, label=TRUE, verbose=FALSE)


Version Informaion

sessionInfo()

Funding

This project has been funded by NSF awards: PGRP-1546879{target="_blank"}, PGRP-1810468{target="_blank"}, PGRP-1936492{target="_blank"}.

References



jianhaizhang/spatialHeatmap documentation built on April 21, 2024, 7:43 a.m.