Package 'dominoSignal'

Title: Cell Communication Analysis for Single Cell RNA Sequencing
Description: dominoSignal is a package developed to analyze cell signaling through ligand - receptor - transcription factor networks in scRNAseq data. It takes as input information transcriptomic data, requiring counts, z-scored counts, and cluster labels, as well as information on transcription factor activation (such as from SCENIC) and a database of ligand and receptor pairings (such as from CellPhoneDB). This package creates an object storing ligand - receptor - transcription factor linkages by cluster and provides several methods for exploring, summarizing, and visualizing the analysis.
Authors: Christopher Cherry [aut] , Jacob T Mitchell [aut, cre] , Sushma Nagaraj [aut] , Kavita Krishnan [aut] , Dmitrijs Lvovs [aut], Elana Fertig [ctb] , Jennifer Elisseeff [ctb]
Maintainer: Jacob T Mitchell <[email protected]>
License: GPL-3 | file LICENSE
Version: 0.99.4
Built: 2024-09-06 03:25:28 UTC
Source: https://github.com/bioc/dominoSignal

Help Index

Adds a column to the RL signaling data frame.

Description

This function adds a column to the internal rl 'map' used to map all receptor and receptor complexes to all ligand and ligand complexes.

Usage

add_rl_column(map, map_ref, conv, new_name)

Arguments

map

RL signaling data frame.
map_ref

Name of column to match new data to
conv

Data frame matching current data in map to new data.
new_name

Name of new column to be created in RL map

Value

An updated RL signaling data frame

Examples

example(create_rl_map_cellphonedb, echo = FALSE)
lr_name <- data.frame("abbrev" = c("L", "R"), "full" = c("Ligand", "Receptor"))
rl_map_expanded <- add_rl_column(map = rl_map_tiny, map_ref = "type_A",
conv = lr_name, new_name = "type_A_full")

Calculate a signaling network for a domino object

Description

This function calculates a signaling network. It requires a domino object preprocessed from create_domino and returns a domino object prepared for plotting with the various plotting functions in this package.

Usage

build_domino(
  dom,
  max_tf_per_clust = 5,
  min_tf_pval = 0.01,
  max_rec_per_tf = 5,
  rec_tf_cor_threshold = 0.15,
  min_rec_percentage = 0.1
)

Arguments

dom

Domino object from create_domino().
max_tf_per_clust

Maximum number of transcription factors called active in a cluster.
min_tf_pval

Minimum p-value from differential feature score test to call a transcription factor active in a cluster.
max_rec_per_tf

Maximum number of receptors to link to each transcription factor.
rec_tf_cor_threshold

Minimum Spearman correlation used to consider a receptor linked with a transcription factor. Increasing this will decrease the number of receptors linked to each transcription factor.
min_rec_percentage

Minimum percentage of cells in cluster expressing a receptor for the receptor to be linked to trancription factors in that cluster.

Value

A domino object with a signaling network built

Examples

example(create_domino, echo = FALSE)

#a relaxed example
pbmc_dom_built_tiny <- build_domino(
 dom = pbmc_dom_tiny, min_tf_pval = .05, max_tf_per_clust = Inf,
 max_rec_per_tf = Inf, rec_tf_cor_threshold = .1, min_rec_percentage = 0.01
)

CellPhoneDB subset

Description

A list of four subsets of CellPhoneDB data.

Usage

data("CellPhoneDB")

Format

A list of:

genes_tiny

A subet of CellPhoneDB gene_input.csv

proteins_tiny

A subset of CellPhoneDB protein_input.csv

complexes_tiny

A subset of CellPhoneDB complex_input.csv

interactions_tiny

A subset of CellPhoneDB interaction_input.csv

Source

https://github.com/ventolab/cellphonedb-data/archive/refs/tags/v4.0.0.tar.gz

Plot expression of a receptor's ligands by other cell types as a chord plot

Description

Creates a chord plot of expression of ligands that can activate a specified receptor where chord widths correspond to mean ligand expression by the cluster.

Usage

circos_ligand_receptor(
  dom,
  receptor,
  ligand_expression_threshold = 0.01,
  cell_idents = NULL,
  cell_colors = NULL
)

Arguments

dom

Domino object that has undergone network building with build_domino()
receptor

Name of a receptor active in at least one cell type in the domino object
ligand_expression_threshold

Minimum mean expression value of a ligand by a cell type for a chord to be rendered between the cell type and the receptor
cell_idents

Vector of cell types from cluster assignments in the domino object to be included in the plot.
cell_colors

Named vector of color names or hex codes where names correspond to the plotted cell types and the color values

Value

Renders a circos plot to the active graphics device

Examples

example(build_domino, echo = FALSE)
#basic usage
circos_ligand_receptor(pbmc_dom_built_tiny, receptor = "CXCR3")
#specify colors
cols = c("red", "orange", "green")
names(cols) = dom_clusters(pbmc_dom_built_tiny)
circos_ligand_receptor(pbmc_dom_built_tiny, receptor = "CXCR3", cell_colors = cols)

Create a heatmap of correlation between receptors and transcription factors

Description

Creates a heatmap of correlation values between receptors and transcription factors either with boolean threshold or with continuous values displayed

Usage

cor_heatmap(
  dom,
  bool = FALSE,
  bool_thresh = 0.15,
  title = TRUE,
  feats = NULL,
  recs = NULL,
  mark_connections = FALSE,
  ...
)

Arguments

dom

Domino object with network built (build_domino())
bool

Boolean indicating whether the heatmap should be continuous or boolean. If boolean then bool_thresh will be used to determine how to define activity as positive or negative.
bool_thresh

Numeric indicating the threshold separating 'on' or 'off' for feature activity if making a boolean heatmap.
title

Either a string to use as the title or a boolean describing whether to include a title. In order to pass the 'main' parameter to ComplexHeatmap::Heatmap() you must set title to FALSE.
feats

Either a vector of features to include in the heatmap or 'all' for all features. If left NULL then the features selected for the signaling network will be shown.
recs

Either a vector of receptors to include in the heatmap or 'all' for all receptors. If left NULL then the receptors selected in the signaling network connected to the features plotted will be shown.
mark_connections

Boolean indicating whether to add an 'x' in cells where there is a connected receptor or TF. Default FALSE.
...

Other parameters to pass to ComplexHeatmap::Heatmap() . Note that to use the 'main' parameter of ComplexHeatmap::Heatmap() you must set title = FALSE and to use 'annCol' or 'annColors' ann_cols must be FALSE.

Value

A heatmap rendered to the active graphics device

Examples

example(build_domino, echo = FALSE)
#basic usage
cor_heatmap(pbmc_dom_built_tiny, title = "PBMC R-TF Correlations")
#show correlations above a specific value
cor_heatmap(pbmc_dom_built_tiny, bool = TRUE, bool_thresh = 0.1)
#identify combinations that are connected
cor_heatmap(pbmc_dom_built_tiny, bool = FALSE, mark_connections = TRUE)

Create a correlation plot between TF and receptor

Description

Create a correlation plot between transcription factor activation score and receptor expression

Usage

cor_scatter(dom, tf, rec, remove_rec_dropout = TRUE, ...)

Arguments

dom

Domino object with network built (build_domino())
tf

Target TF for plottting AUC score
rec

Target receptor for plotting expression
remove_rec_dropout

Whether to remove cells with zero expression for plot. This should match the same setting as in build_domino().
...

Other parameters to pass to ggpubr::ggscatter().

Value

A ggplot scatter plot rendered in the active graphics device

Examples

example(build_domino, echo = FALSE)
cor_scatter(pbmc_dom_built_tiny, "FLI1","CXCR3")

Count occurrences of linkages across multiple domino results from a linkage summary

Description

Count occurrences of linkages across multiple domino results from a linkage summary

Usage

count_linkage(
  linkage_summary,
  cluster,
  group.by = NULL,
  linkage = "rec_lig",
  subject_names = NULL
)

Arguments

linkage_summary

a linkage_summary() object
cluster

the name of the cell cluster being compared across multiple domino results
group.by

the name of the column in linkage_summary@subject_meta by which to group subjects for counting. If NULL, only total counts of linkages for linkages in the cluster across all subjects is given.
linkage

a stored linkage from the domino object. Can compare any of 'tfs', 'rec', 'incoming_lig', 'tfs_rec', or 'rec_lig'
subject_names

a vector of subject_names from the linkage_summary to be compared. If NULL, all subject_names in the linkage summary are included in counting.

Value

A data frame with columns for the unique linkage features and the counts of how many times the linkage occured across the compared domino results. If group.by is used, counts of the linkages are also provided as columns named by the unique values of the group.by variable.

Examples

count_linkage(
  linkage_summary = mock_linkage_summary(), cluster = "C1", 
  group.by = "group", linkage = "rec")

Create a domino object and prepare it for network construction

Description

This function reads in a receptor ligand signaling database, cell level features of some kind (ie. output from pySCENIC), z-scored single cell data, and cluster id for single cell data, calculates a correlation matrix between receptors and other features (this is transcription factor module scores if using pySCENIC), and finds features enriched by cluster. It will return a domino object prepared for build_domino(), which will calculate a signaling network.

Usage

create_domino(
  rl_map,
  features,
  counts = NULL,
  z_scores = NULL,
  clusters = NULL,
  use_clusters = TRUE,
  tf_targets = NULL,
  verbose = TRUE,
  use_complexes = TRUE,
  rec_min_thresh = 0.025,
  remove_rec_dropout = TRUE,
  tf_selection_method = "clusters",
  tf_variance_quantile = 0.5
)

Arguments

rl_map

Data frame where each row describes a receptor-ligand interaction with required columns gene_A & gene_B including the gene names for the receptor and ligand and type_A & type_B annotating if genes A and B are a ligand (L) or receptor (R)
features

Either a path to a csv containing cell level features of interest (ie. the auc matrix from pySCENIC) or named matrix with cells as columns and features as rows.
counts

Counts matrix for the data. This is only used to threshold receptors on dropout.
z_scores

Matrix containing z-scored expression data for all cells with cells as columns and features as rows.
clusters

Named factor containing cell cluster with names as cells.
use_clusters

Boolean indicating whether to use clusters.
tf_targets

Optional. A list where names are transcription factors and the stored values are character vectors of genes in the transcription factor's regulon.
verbose

Boolean indicating whether or not to print progress during computation.
use_complexes

Boolean indicating whether you wish to use receptor/ligand complexes in the receptor ligand signaling database. If FALSE, receptor/ligand pairs where either functions as a protein complex will not be considered when constructing the signaling network.
rec_min_thresh

Minimum expression level of receptors by cell. Default is 0.025 or 2.5 percent of all cells in the data set. This is important when calculating correlation to connect receptors to transcription activation. If this threshold is too low then correlation calculations will proceed with very few cells with non-zero expression.
remove_rec_dropout

Whether to remove receptors with 0 expression counts when calculating correlations. This can reduce false positive correlation calculations when receptors have high dropout rates.
tf_selection_method

Selection of which method to target transcription factors. If 'clusters' then differential expression for clusters will be calculated. If 'variable' then the most variable transcription factors will be selected. If 'all' then all transcription factors in the feature matrix will be used. Default is 'clusters'. Note that if you wish to use clusters for intercellular signaling downstream to MUST choose clusters.
tf_variance_quantile

What proportion of variable features to take if using variance to threshold features. Default is 0.5. Higher numbers will keep more features. Ignored if tf_selection_method is not 'variable'

Value

A domino object

Examples

example(create_rl_map_cellphonedb, echo = FALSE)
example(create_regulon_list_scenic, echo = FALSE)
data(SCENIC)
data(PBMC)

pbmc_dom_tiny <- create_domino(
 rl_map = rl_map_tiny, features = SCENIC$auc_tiny,
 counts = PBMC$RNA_count_tiny, z_scores = PBMC$RNA_zscore_tiny,
 clusters = PBMC$clusters_tiny, tf_targets = regulon_list_tiny,
 use_clusters = TRUE, use_complexes = TRUE, remove_rec_dropout = FALSE,
 verbose = FALSE
 )

pbmc_dom_tiny_no_clusters <- create_domino(
 rl_map = rl_map_tiny, features = SCENIC$auc_tiny,
 counts = PBMC$RNA_count_tiny, z_scores =PBMC$RNA_zscore_tiny,
 clusters = PBMC$clusters_tiny, tf_targets = regulon_list_tiny,
 use_clusters = FALSE, use_complexes = FALSE,
 rec_min_thresh = 0.1, remove_rec_dropout = TRUE,
 tf_selection_method = "all",
 verbose = FALSE
 )

Create a list of genes in regulons inferred by SCENIC

Description

Generates a list of transcription factors and the genes targeted by the transcription factor as part of their regulon inferred by pySCENIC

Usage

create_regulon_list_scenic(regulons)

Arguments

regulons

Data frame or file path to the table of the output of the ctx function from pySCENIC

Value

A list where names are transcription factors and the stored values are character vectors of genes in the inferred regulons

Examples

data(SCENIC)
regulon_list_tiny <- create_regulon_list_scenic(regulons = SCENIC$regulons_tiny)

Create a receptor - ligand map from a CellPhoneDB signaling database

Description

Generates a data frame of ligand-receptor interactions from a CellPhoneDB database annotating the genes encoding the interacting ligands and receptors to be queried in transcriptomic data.

Usage

create_rl_map_cellphonedb(
  genes,
  proteins,
  interactions,
  complexes = NULL,
  database_name = "CellPhoneDB",
  gene_conv = NULL,
  gene_conv_host = "https://www.ensembl.org",
  alternate_convert = FALSE,
  alternate_convert_table = NULL
)

Arguments

genes

data frame or file path to table of gene names in uniprot, hgnc_symbol, or ensembl format in CellPhoneDB database format
proteins

data frame or file path to table of protein features in CellPhoneDB format
interactions

data frame or file path to table of protein-protein interactions in CellPhoneDB format
complexes

optional: data frame or file path to table of protein complexes in CellPhoneDB format
database_name

name of the database being used, stored in output
gene_conv

a tuple of (from, to) or (source, target) if gene conversion to orthologs is desired; options are ENSMUSG, ENSG, MGI, or HGNC
gene_conv_host

host for conversion; default ensembl, could also use mirrors if desired
alternate_convert

boolean if you would like to use a non-ensembl method of conversion (must supply table; not recommended, use only if ensembl is down)
alternate_convert_table

supplied table for non-ensembl method of conversion

Value

Data frame where each row describes a possible receptor-ligand interaction

Examples

data(CellPhoneDB)
rl_map_tiny <- create_rl_map_cellphonedb(genes = CellPhoneDB$genes_tiny,
 proteins = CellPhoneDB$proteins_tiny,
 interactions = CellPhoneDB$interactions_tiny,
 complexes =CellPhoneDB$complexes_tiny)

Access clusters

Description

A function to pull cluster information from a domino object

Usage

dom_clusters(dom, labels = FALSE)

Arguments

dom

a domino object that has been created with create_domino()
labels

a boolean for whether to return the cluster labels for each cell or the clusters used for inferring communication

Value

A vector containing either the names of the clusters used OR factors of the cluster label for each individual cell

Examples

example(build_domino, echo = FALSE)
cluster_names <- dom_clusters(pbmc_dom_built_tiny)
cell_cluster_label <- dom_clusters(pbmc_dom_built_tiny, labels = TRUE)

Access correlations

Description

A function to pull receptor-transcription factor correlations from a domino object

Usage

dom_correlations(dom, type = "rl")

Arguments

dom

a domino object that has been created with create_domino()
type

either "rl" or "complex", to select between the receptor-ligand or complex correlation matrix

Value

A matrix containing the correlation values for each receptor (row) by transcription factor (column)

Examples

example(build_domino, echo = FALSE)
cor_matrix <- dom_correlations(pbmc_dom_built_tiny, "rl")

Access counts

Description

A function to pull gene expression from a domino object

Usage

dom_counts(dom)

Arguments

dom

a domino object that has been created with create_domino()

Value

A matrix containing the gene expression values for each gene (row) by cell (column)

Examples

example(build_domino, echo = FALSE)
counts <- dom_counts(pbmc_dom_built_tiny)

Access database

Description

A function to pull database information from a domino object

Usage

dom_database(dom, name_only = TRUE)

Arguments

dom

a domino object that has been created
name_only

a boolean for whether to return only the name of the database used or the entire database that is stored. Default TRUE.

Value

A vector of unique databases used in building the domino object OR a data frame that includes the database information used in the domino object creation

Examples

example(build_domino, echo = FALSE)
database_name <- dom_database(pbmc_dom_built_tiny)
full_database <- dom_database(pbmc_dom_built_tiny, name_only = FALSE)

Access differential expression

Description

A function to pull differential expression p-values from a domino object

Usage

dom_de(dom)

Arguments

dom

a domino object that has been created with create_domino()

Value

A matrix containing the p-values for differential expression of transcription factors (rows) in each cluster (columns)

Examples

example(build_domino, echo = FALSE)
de_mat <- dom_de(pbmc_dom_built_tiny)

Access build information

Description

A function to pull the parameters used when running build_domino() from a domino object

Usage

dom_info(dom)

Arguments

dom

a domino object that has been created with create_domino()

Value

A list containing booleans for whether the object has been created and built and a list of the build parameters that were used in build_domino() to infer the signaling network

Examples

example(build_domino, echo = FALSE)
build_details <- dom_info(pbmc_dom_built_tiny)

Access linkages

Description

A function to pull linkages from a domino object

Usage

dom_linkages(
  dom,
  link_type = c("complexes", "receptor-ligand", "tf-target", "tf-receptor", "receptor",
    "incoming-ligand"),
  by_cluster = FALSE
)

Arguments

dom

a domino object that has been created with create_domino()
link_type

one value (out of "complexes", "receptor-ligand", "tf-target", "tf-receptor", "receptor", "incoming-ligand") used to select the desired type of linkage
by_cluster

a boolean to indicate whether the linkages should be returned overall or by cluster

Value

A list containing linkages between some combination of receptors, ligands, transcription factors, and clusters

Examples

example(build_domino, echo = FALSE)
complexes <- dom_linkages(pbmc_dom_built_tiny, "complexes")
tf_rec_by_cluster <- dom_linkages(pbmc_dom_built_tiny, "tf-receptor", TRUE)

Access all features, receptors, or ligands present in a signaling network.

Description

This function collates all of the features, receptors, or ligands found in a signaling network anywhere in a list of clusters. This can be useful for comparing signaling networks across two separate conditions. In order to run this build_domino() must be run on the object previously.

Usage

dom_network_items(dom, clusters = NULL, return = NULL)

Arguments

dom

a domino object containing a signaling network (i.e. build_domino() was run)
clusters

vector indicating clusters to collate network items from. If left as NULL then all clusters will be included.
return

string indicating whether to collate "features", "receptors", or "ligands". If "all" then a list of all three will be returned.

Value

A vector containing all features, receptors, or ligands in the data set or a list containing all three.

Examples

example(build_domino, echo = FALSE)
monocyte_receptors <- dom_network_items(pbmc_dom_built_tiny, "CD14_monocyte", "receptors")
all_tfs <- dom_network_items(pbmc_dom_built_tiny, return = "features")

Access signaling

Description

A function to pull signaling matrices from a domino object

Usage

dom_signaling(dom, cluster = NULL)

Arguments

dom

a domino object that has been created with create_domino()
cluster

either NULL to indicate global signaling or a specific cluster for which a signaling matrix is desired

Value

A data frame containing the signaling score through each ligand (row) by each cluster (column) OR a data frame containing the global summed signaling scores between receptors (rows) and ligands (columns) of each cluster

Examples

example(build_domino, echo = FALSE)
monocyte_signaling <- dom_signaling(pbmc_dom_built_tiny, cluster = "CD14_monocyte")

Access transcription factor activation

Description

A function to pull transcription factor activation scores from a domino object

Usage

dom_tf_activation(dom)

Arguments

dom

a domino object that has been created with create_domino()

Value

A matrix containing the transcription factor activation scores for each TF (row) by cell (column)

Examples

example(build_domino, echo = FALSE)
tf_activation <- dom_tf_activation(pbmc_dom_built_tiny)

Access z-scores

Description

A function to pull z-scored expression from a domino object

Usage

dom_zscores(dom)

Arguments

dom

a domino object that has been created with create_domino()

Value

A matrix containing the z-scored gene expression values for each gene (row) by cell (column)

Examples

example(build_domino, echo = FALSE)
zscores <- dom_zscores(pbmc_dom_built_tiny)

The domino class

Description

The domino class contains all information necessary to calculate receptor-ligand signaling. It contains z-scored expression, cell cluster labels, feature values, and a referenced receptor-ligand database formatted as a receptor-ligand map. Calculated intermediate values are also stored.

Value

An instance of class domino

Slots

db_info

List of data sets from ligand - receptor database

counts

Raw count gene expression data

z_scores

Matrix of z-scored expression data with cells as columns

clusters

Named factor with cluster identity of each cell

features

Matrix of features (TFs) to correlate receptor - ligand expression with. Cells are columns and features are rows.

cor

Correlation matrix of receptor expression to features.

linkages

List of lists containing info linking cluster->tf->rec->lig

clust_de

Data frame containing differential expression results for features by cluster.

misc

List of miscellaneous info pertaining to run parameters etc.

cl_signaling_matrices

Incoming signaling matrix for each cluster

signaling

Signaling matrix between all clusters.

Create a heatmap of features organized by cluster

Description

Creates a heatmap of transcription factor activation scores by cells grouped by cluster.

Usage

feat_heatmap(
  dom,
  feats = NULL,
  bool = FALSE,
  bool_thresh = 0.2,
  title = TRUE,
  norm = FALSE,
  cols = NULL,
  ann_cols = TRUE,
  min_thresh = NULL,
  max_thresh = NULL,
  ...
)

Arguments

dom

Domino object with network built (build_domino())
feats

Either a vector of features to include in the heatmap or 'all' for all features. If left NULL then the features selected for the signaling network will be shown.
bool

Boolean indicating whether the heatmap should be continuous or boolean. If boolean then bool_thresh will be used to determine how to define activity as positive or negative.
bool_thresh

Numeric indicating the threshold separating 'on' or 'off' for feature activity if making a boolean heatmap.
title

Either a string to use as the title or a boolean describing whether to include a title. In order to pass the 'main' parameter to ComplexHeatmap::Heatmap() you must set title to FALSE.
norm

Boolean indicating whether or not to normalize the transcrption factors to their max value.
cols

Named vector of colors to annotate cells by cluster color. Values are taken as colors and names as cluster. If left as NULL then default ggplot colors will be generated.
ann_cols

Boolean indicating whether to include cell cluster as a column annotation. Colors can be defined with cols. If FALSE then custom annotations can be passed to ComplexHeatmap::Heatmap().
min_thresh

Minimum threshold for color scaling if not a boolean heatmap
max_thresh

Maximum threshold for color scaling if not a boolean heatmap
...

Other parameters to pass to ComplexHeatmap::Heatmap() . Note that to use the 'main' parameter of ComplexHeatmap::Heatmap() you must set title = FALSE and to use 'annCol' or 'annColors' ann_cols must be FALSE.

Value

A heatmap rendered to the active graphics device

Examples

#basic usage
example(build_domino, echo = FALSE)
feat_heatmap(pbmc_dom_built_tiny)
#using thresholds
feat_heatmap(
 pbmc_dom_built_tiny, min_thresh = 0.1, 
 max_thresh = 0.6, norm = TRUE, bool = FALSE)

Create a gene association network

Description

Create a gene association network for genes from a given cluster. The selected cluster acts as the receptor for the gene association network, so only ligands, receptors, and features associated with the receptor cluster will be included in the plot.

Usage

gene_network(
  dom,
  clust = NULL,
  OutgoingSignalingClust = NULL,
  class_cols = c(lig = "#FF685F", rec = "#47a7ff", feat = "#39C740"),
  cols = NULL,
  lig_scale = 1,
  layout = "grid",
  ...
)

Arguments

dom

Domino object with network built (build_domino())
clust

Receptor cluster to create the gene association network for. A vector of clusters may be provided.
OutgoingSignalingClust

Vector of clusters to plot the outgoing signaling from
class_cols

Named vector of colors used to color classes of vertices. Values must be colors and names must be classes ('rec', 'lig', and 'feat' for receptors, ligands, and features.).
cols

Named vector of colors for individual genes. Genes not included in this vector will be colored according to class_cols.
lig_scale

FALSE or a numeric value to scale the size of ligand vertices based on z-scored expression in the data set.
layout

Type of layout to use. Options are 'grid', 'random', 'sphere', 'circle', 'fr' for Fruchterman-Reingold force directed layout, and 'kk' for Kamada Kawai for directed layout.
...

Other parameters to pass to plot() with an igraph object. See igraph manual for options.

Value

An igraph plot rendered to the active graphics device

Examples

#basic usage
example(build_domino, echo = FALSE)
gene_network(
 pbmc_dom_built_tiny, clust = "CD8_T_cell", 
 OutgoingSignalingClust = "CD14_monocyte")

Create a cluster incoming signaling heatmap

Description

Creates a heatmap of a cluster incoming signaling matrix. Each cluster has a list of ligands capable of activating its enriched transcription factors. The function creates a heatmap of cluster average expression for all of those ligands. A list of all cluster incoming signaling matrices can be found in the cl_signaling_matrices slot of a domino option as an alternative to this plotting function.

Usage

incoming_signaling_heatmap(
  dom,
  rec_clust,
  clusts = NULL,
  min_thresh = -Inf,
  max_thresh = Inf,
  scale = "none",
  normalize = "none",
  title = TRUE,
  ...
)

Arguments

dom

Domino object with network built (build_domino())
rec_clust

Which cluster to select as the receptor. Must match naming of clusters in the domino object.
clusts

Vector of clusters to be included. If NULL then all clusters are used.
min_thresh

Minimum signaling threshold for plotting. Defaults to -Inf for no threshold.
max_thresh

Maximum signaling threshold for plotting. Defaults to Inf for no threshold.
scale

How to scale the values (after thresholding). Options are 'none', 'sqrt' for square root, or 'log' for log10.
normalize

Options to normalize the matrix. Accepted inputs are 'none' for no normalization, 'rec_norm' to normalize to the maximum value with each receptor cluster, or 'lig_norm' to normalize to the maximum value within each ligand cluster
title

Either a string to use as the title or a boolean describing whether to include a title. In order to pass the 'main' parameter to ComplexHeatmap::Heatmap() you must set title to FALSE.
...

Other parameters to pass to ComplexHeatmap::Heatmap(). Note that to use the 'column_title' parameter of ComplexHeatmap::Heatmap() you must set title = FALSE

Value

a Heatmap rendered to the active graphics device

Examples

example(build_domino, echo = FALSE)
#incoming signaling of the CD8  T cells
incoming_signaling_heatmap(pbmc_dom_built_tiny, "CD8_T_cell")

The domino linkage summary class

Description

The linkage summary class contains linkages established in multiple domino objects through gene regulatory network inference and reference to receptor- ligand data bases. A data frame summarizing meta features that describe the domino objects compared in the linkage summary facilitates comparisons of established linkages and differential signaling interactions across categorical sample covariates.

Value

an instance of class linkage_summary

Slots

subject_names

unique names for each domino result included in the summary

subject_meta

data.frame with each row describing one subject and columns describing features of the subjects by which to draw comparisons of signaling networks

subject_linkages

nested list of linkages inferred for each subject. Lists are stored in a heirarchical structure of subject-cluster-linkage where linkages include transcription factors (tfs), linkages between transcription factors and receptors (tfs_rec), active receptors (rec), possible receptor-ligand interactions (rec_lig), and incoming ligands (incoming_lig)

Calculate mean ligand expression as a data frame for plotting in circos plot

Description

Creates a data frame of mean ligand expression for use in plotting a circos plot of ligand expression and saving tables of mean expression. us

Usage

mean_ligand_expression(x, ligands, cell_ident, cell_barcodes, destination)

Arguments

x

Gene by cell expression matrix
ligands

Character vector of ligand genes to be quantified
cell_ident

Vector of cell type (identity) names for which to calculate mean ligand gene expression
cell_barcodes

Vector of cell barcodes (colnames of x) belonging to cell_ident to calculate mean expression across
destination

Name of the receptor with which each ligand interacts

Value

A data frame of ligand expression targeting the specified receptor

Examples

example(build_domino, echo = FALSE)
counts <- dom_counts(pbmc_dom_built_tiny)
mean_exp <- mean_ligand_expression(counts,
 ligands = c("PTPRC", "FASLG"), cell_ident = "CD14_monocyte",
 cell_barcodes = colnames(counts), destination = "FAS")

Create a mock linkage summary object

Description

Create a mock linkage summary object

Usage

mock_linkage_summary()

Value

obj a linkage summary object

PBMC RNAseq data subset

Description

A subset of the results of PBMC RNA-seq data.

Usage

data("PBMC")

Format

A list of::

RNA_count_tiny

A subset of PBMC RNA-seq data: counts assay

RNA_zscore_tiny

A subset of PBMC RNA-seq data: zscore assay

clusters_tiny

A subset of PBMC RNA-seq data: clusters as defined by cell_type

Source

https://zenodo.org/records/10951634/files/pbmc3k_sce.rds

Plot differential linkages among domino results ranked by a comparative statistic

Description

Plot differential linkages among domino results ranked by a comparative statistic

Usage

plot_differential_linkages(
  differential_linkages,
  test_statistic,
  stat_range = c(0, 1),
  stat_ranking = c("ascending", "descending"),
  group_palette = NULL
)

Arguments

differential_linkages

a data frame output from the test_differential_linkages() function
test_statistic

column name of differential_linkages where the test statistic used for ranking linkages is stored (ex. 'p.value')
stat_range

a two value vector of the minimum and maximum values of test_statistic for plotting linkage features
stat_ranking

'ascending' (lowest value of test statisic is colored red and plotted at the top) or 'descending' (highest value of test statistic is colored red and plotted at the top).
group_palette

a named vector of colors to use for each group being compared

Value

A heatmap-class object of features ranked by test_statistic annotated with the proportion of subjects that showed active linkage of the features.

Examples

example(build_domino, echo = FALSE)
example(test_differential_linkages, echo = FALSE)
plot_differential_linkages(
 differential_linkages = tiny_differential_linkage_c1,
 test_statistic = "p.value",
 stat_ranking = "ascending"
)

Print domino object

Description

Prints a summary of a domino object

Usage

## S4 method for signature 'domino'
print(x, ...)

Arguments

x

A domino object
...

Additional arguments to be passed to other methods

Value

A printed description of the number of cells and clusters in the domino object

Examples

example(build_domino, echo = FALSE)
print(pbmc_dom_built_tiny)

Renames clusters in a domino object

Description

This function renames the clusters used to build a domino object

Usage

rename_clusters(dom, clust_conv, warning = FALSE)

Arguments

dom

a domino object to rename clusters in
clust_conv

named vector of conversions from old to new clusters. Values are taken as new clusters IDs and names as old cluster IDs.
warning

logical. If TRUE, will warn if a cluster is not found in the conversion table. Default is FALSE.

Value

A domino object with clusters renamed in all applicable slots.

Examples

example(build_domino, echo = FALSE)
new_clust <- c("CD8_T_cell" = "CD8+ T Cells",
 "CD14_monocyte" = "CD14+ Monocytes", "B_cell" = "B Cells")
pbmc_dom_built_tiny <- rename_clusters(pbmc_dom_built_tiny, new_clust)

SCENIC AUC subset

Description

A subset of SCENIC AUCs as applied to PBMC data.

Usage

data("SCENIC")

Format

A list of:

auc_tiny

A subset of SCENIC AUCs

regulons_tiny

A subset of SCENIC regulons

Source

https://zenodo.org/records/10951634/files

Show domino object information

Description

Shows content overview of domino object

Usage

## S4 method for signature 'domino'
show(object)

Arguments

object

A domino object

Value

A printed description of cell numbers and clusters in the object

Examples

example(build_domino, echo = FALSE)
show(pbmc_dom_built_tiny)

Create a network heatmap

Description

Creates a heatmap of the signaling network. Alternatively, the network matrix can be accessed directly in the signaling slot of a domino object using the dom_signaling() function.

Usage

signaling_heatmap(
  dom,
  clusts = NULL,
  min_thresh = -Inf,
  max_thresh = Inf,
  scale = "none",
  normalize = "none",
  ...
)

Arguments

dom

domino object with network built (build_domino())
clusts

vector of clusters to be included. If NULL then all clusters are used.
min_thresh

minimum signaling threshold for plotting. Defaults to -Inf for no threshold.
max_thresh

maximum signaling threshold for plotting. Defaults to Inf for no threshold.
scale

how to scale the values (after thresholding). Options are 'none', 'sqrt' for square root, or 'log' for log10.
normalize

options to normalize the matrix. Normalization is done after thresholding and scaling. Accepted inputs are 'none' for no normalization, 'rec_norm' to normalize to the maximum value with each receptor cluster, or 'lig_norm' to normalize to the maximum value within each ligand cluster
...

other parameters to pass to ComplexHeatmap::Heatmap()

Value

A heatmap rendered to the active graphics device

Examples

example(build_domino, echo = FALSE)
#basic usage
signaling_heatmap(pbmc_dom_built_tiny)
#scale
signaling_heatmap(pbmc_dom_built_tiny, scale = "sqrt")
#normalize
signaling_heatmap(pbmc_dom_built_tiny, normalize = "rec_norm")

Create a cluster to cluster signaling network diagram

Description

Creates a network diagram of signaling between clusters. Nodes are clusters and directed edges indicate signaling from one cluster to another. Edges are colored based on the color scheme of the ligand expressing cluster

Usage

signaling_network(
  dom,
  cols = NULL,
  edge_weight = 0.3,
  clusts = NULL,
  showOutgoingSignalingClusts = NULL,
  showIncomingSignalingClusts = NULL,
  min_thresh = -Inf,
  max_thresh = Inf,
  normalize = "none",
  scale = "sq",
  layout = "circle",
  scale_by = "rec_sig",
  vert_scale = 3,
  plot_title = NULL,
  ...
)

Arguments

dom

a domino object with network built (build_domino())
cols

named vector indicating the colors for clusters. Values are colors and names must match clusters in the domino object. If left as NULL then ggplot colors are generated for the clusters
edge_weight

weight for determining thickness of edges on plot. Signaling values are multiplied by this value
clusts

vector of clusters to be included in the network plot
showOutgoingSignalingClusts

vector of clusters to plot the outgoing signaling from
showIncomingSignalingClusts

vector of clusters to plot the incoming signaling on
min_thresh

minimum signaling threshold. Values lower than the threshold will be set to the threshold. Defaults to -Inf for no threshold
max_thresh

maximum signaling threshold for plotting. Values higher than the threshold will be set to the threshold. Defaults to Inf for no threshold
normalize

options to normalize the signaling matrix. Accepted inputs are 'none' for no normalization, 'rec_norm' to normalize to the maximum value with each receptor cluster, or 'lig_norm' to normalize to the maximum value within each ligand cluster
scale

how to scale the values (after thresholding). Options are 'none', 'sqrt' for square root, 'log' for log10, or 'sq' for square
layout

type of layout to use. Options are 'random', 'sphere', 'circle', 'fr' for Fruchterman-Reingold force directed layout, and 'kk' for Kamada Kawai for directed layout
scale_by

how to size vertices. Options are 'lig_sig' for summed outgoing signaling, 'rec_sig' for summed incoming signaling, and 'none'. In the former two cases the values are scaled with asinh after summing all incoming or outgoing signaling
vert_scale

integer used to scale size of vertices with our without variable scaling from size_verts_by.
plot_title

text for the plot's title.
...

other parameters to be passed to plot when used with an igraph object.

Value

An igraph plot rendered to the active graphics device

Examples

example(build_domino, echo = FALSE)
#basic usage
signaling_network(pbmc_dom_built_tiny, edge_weight = 2)
# scaling, thresholds, layouts, selecting clusters
signaling_network(
 pbmc_dom_built_tiny, showOutgoingSignalingClusts = "CD14_monocyte", 
 scale = "none", norm = "none", layout = "fr", scale_by = "none", 
 vert_scale = 5, edge_weight = 2)

Summarize linkages from multiple domino objects

Description

Creates a linkage_summary() object storing the linkages learned in different domino objects as nested lists to facilitate comparisons of networks learned by domino across subject covariates.

Usage

summarize_linkages(domino_results, subject_meta, subject_names = NULL)

Arguments

domino_results

list of domino result with one domino object per subject. Names from the list must match subject_names
subject_meta

data frame that includes the subject features by which the objects could be grouped. The first column should must be subject names
subject_names

vector of subject names in domino_results. If NULL, defaults to first column of subject_meta.

Value

A linkage summary class object consisting of nested lists of the active transcription factors, active receptors, and incoming ligands for each cluster across multiple domino results

Examples

example(build_domino, echo = FALSE)

#create alternative clustering by shuffling cluster assignments
clusters_tiny_alt <- setNames(
  PBMC$clusters_tiny[c(121:240, 1:120, 241:360)], 
  names(PBMC$clusters_tiny)
)
clusters_tiny_alt <- as.factor(clusters_tiny_alt)

#build an alternative domino object
pbmc_dom_tiny_alt <- create_domino(
  rl_map = rl_map_tiny,
  features = SCENIC$auc_tiny,
  counts = PBMC$RNA_count_tiny,
  z_scores = PBMC$RNA_zscore_tiny,
  clusters = clusters_tiny_alt,
  tf_targets = regulon_list_tiny,
  use_clusters = TRUE,
  use_complexes = TRUE,
  remove_rec_dropout = FALSE
)

pbmc_dom_built_tiny_alt <- build_domino(
  dom = pbmc_dom_tiny_alt,
  min_tf_pval = .05,
  max_tf_per_clust = Inf,
  max_rec_per_tf = Inf,
  rec_tf_cor_threshold = .1,
  min_rec_percentage = 0.01
)

#create a list of domino objects
dom_ls <- list(
 dom1 = pbmc_dom_built_tiny,
 dom2 = pbmc_dom_built_tiny_alt
)

#compare the linkages across the two domino objects
meta_df <- data.frame("ID" = c("dom1", "dom2"), "group" = c("A", "B"))
summarize_linkages(
 domino_results = dom_ls, subject_meta = meta_df,
 subject_names = meta_df$ID
)

Statistical test for differential linkages across multiple domino results

Description

Statistical test for differential linkages across multiple domino results

Usage

test_differential_linkages(
  linkage_summary,
  cluster,
  group.by,
  linkage = "rec_lig",
  subject_names = NULL,
  test_name = "fishers.exact"
)

Arguments

linkage_summary

a linkage_summary() object
cluster

the name of the cell cluster being compared across multiple domino results
group.by

the name of the column in linkage_summary@subject_meta by which to group subjects for counting.
linkage

a stored linkage from the domino object. Can compare any of 'tfs', 'rec', 'incoming_lig', 'tfs_rec', or 'rec_lig'
subject_names

a vector of subject_names from the linkage_summary to be compared. If NULL, all subject_names in the linkage summary are included in counting.
test_name

the statistical test used for comparison.

  • 'fishers.exact' : Fisher's exact test for the dependence of the proportion of subjects with an active linkage in the cluster on which group the subject belongs to in the group.by variable. Provides an odds ratio, p-value, and a Benjamini-Hochberg FDR-adjusted p-value (p.adj) for each linkage tested.

Value

A data frame of results from the test of the differential linkages. Rows correspond to each linkage tested. Columns correspond to:

  • 'cluster' : the name of the cell cluster being compared

  • 'linkage' : the type of linkage being compared

  • 'group.by' : the grouping variable

  • 'test_name' : the test used for comparison

  • 'feature' : individual linkages compared

  • 'test statistics' : test statistics provided are based on test method. 'fishers.exact' provides a odds ratio, p-value, and fdr-adjusted p-value.

  • 'total_count' : total number of subjects where the linkage is active

  • 'X_count' : number of subjects in each category of group.by (X) where the linkage is active

  • 'total_n' : number of total subjects compared

  • 'X_n' : total number of subjects in each category of group.by (X)

Examples

tiny_differential_linkage_c1 <- test_differential_linkages(
  linkage_summary = mock_linkage_summary(), cluster = "C1", group.by = "group",
  linkage = "rec", test_name = "fishers.exact"
)