Cell-Cell Communication Inference (Source-Target)

Detect interactions between source and target cell types

1 datasets · 14 methods · 2 control methods · 2 metrics

Info

Repository
v1.0.0
MIT

Task info Method info Metric info Dataset info Results

The growing availability of single-cell data has sparked an increased interest in the inference of cell-cell communication (CCC), with an ever-growing number of computational tools developed for this purpose.

Different tools propose distinct preprocessing steps with diverse scoring functions, that are challenging to compare and evaluate. Furthermore, each tool typically comes with its own set of prior knowledge. To harmonize these, Dimitrov et al, 2022 recently developed the LIANA framework, which was used as a foundation for this task.

The challenges in evaluating the tools are further exacerbated by the lack of a gold standard to benchmark the performance of CCC methods. In an attempt to address this, Dimitrov et al use alternative data modalities, including the spatial proximity of cell types and downstream cytokine activities, to generate an inferred ground truth. However, these modalities are only approximations of biological reality and come with their own assumptions and limitations. In time, the inclusion of more datasets with known ground truth interactions will become available, from which the limitations and advantages of the different CCC methods will be better understood.

This subtask evaluates methods in their ability to predict interactions between spatially-adjacent source cell types and target cell types. This subtask focuses on the prediction of interactions from steady-state, or single-context, single-cell data.

Summary

poss_dataset_ids = dataset_info
  .map(d => d.dataset_id)
  .filter(d => results.map(r => r.dataset_id).includes(d))
poss_method_ids = method_info
  .map(d => d.method_id)
  .filter(d => results.map(r => r.method_id).includes(d))
poss_metric_ids = metric_info
  .map(d => d.metric_id)
  .filter(d => results.map(r => Object.keys(r.scaled_scores)).flat().includes(d))

results_long = results.flatMap(d => {
  return Object.entries(d.scaled_scores).map(([metric_id, value]) =>
    ({
      method_id: d.method_id,
      dataset_id: d.dataset_id,
      metric_id: metric_id,
      score: value
    })
  )
}).filter(d => method_ids.includes(d.method_id) && metric_ids.includes(d.metric_id) && dataset_ids.includes(d.dataset_id))

results_resources = results.flatMap(d => {
  return ({
    method_id: d.method_id,
    dataset_id: d.dataset_id,
    ...d.resources
  })
}).filter(d => method_ids.includes(d.method_id) && dataset_ids.includes(d.dataset_id))

function label_time(time) {
  if (time < 1e-5) return "0s";
  if (time < 1) return "<1s";
  if (time < 60) return `${Math.floor(time)}s`;
  if (time < 3600) return `${Math.floor(time / 60)}m`;
  if (time < 3600 * 24) return `${Math.floor(time / 3600)}h`;
  if (time < 3600 * 24 * 7) return `${Math.floor(time / 3600 / 24)}d`;
  return ">7d"; // Assuming missing values are encoded as NaN
}

function label_memory(x_mb, include_mb = true) {
  if (!include_mb && x_mb < 1e3) return "<1G";
  if (x_mb < 1) return "<1M";
  if (x_mb < 1e3) return `${Math.round(x_mb)}M`;
  if (x_mb < 1e6) return `${Math.round(x_mb / 1e3)}G`;
  if (x_mb < 1e9) return `${Math.round(x_mb / 1e6)}T`;
  return ">1P";
}

function aggregate_scores(obj) {
  return d3.mean(obj.map(val => {
    if (val.score === undefined || isNaN(val.score)) return 0;
    return Math.min(1, Math.max(0, val.score))
  }));
}

function mean_na_rm(x) {
  return d3.mean(x.filter(d => !isNaN(d)));
}

function transpose_list_of_objects(list) {
  return Object.fromEntries(Object.keys(list[0]).map(key => [key, list.map(d => d[key])]))
}

overall = d3.groups(results_long, d => d.method_id)
  .map(([method_id, values]) => ({method_id, mean_score: aggregate_scores(values)}))

per_dataset = d3.groups(results_long, d => d.method_id)
  .map(([method_id, values]) => {
    const datasets = d3.groups(values, d => d.dataset_id)
      .map(([dataset_id, values]) => ({["dataset_" + dataset_id]: aggregate_scores(values)}))
      .reduce((a, b) => ({...a, ...b}), {})
    return {method_id, ...datasets}
  })

per_metric = d3.groups(results_long, d => d.method_id)
  .map(([method_id, values]) => {
    const metrics = d3.groups(values, d => d.metric_id)
      .map(([metric_id, values]) => ({["metric_" + metric_id]: aggregate_scores(values)}))
      .reduce((a, b) => ({...a, ...b}), {})
    return {method_id, ...metrics}
  })

resources = d3.groups(results_resources, d => d.method_id)
  .map(([method_id, values]) => {
    const error_pct_oom = d3.mean(values, d => d.exit_code === 137)
    const error_pct_timeout = d3.mean(values, d => d.exit_code === 143)
    const error_pct_error = d3.mean(values, d => d.exit_code > 0) - error_pct_oom - error_pct_timeout
    const error_pct_ok = 1 - error_pct_oom - error_pct_timeout - error_pct_error
    const mean_peak_memory_mb = mean_na_rm(values.map(d => d.peak_memory_mb))
    const mean_disk_read_mb = mean_na_rm(values.map(d => d.disk_read_mb))
    const mean_disk_write_mb = mean_na_rm(values.map(d => d.disk_write_mb))
    const mean_duration_sec = mean_na_rm(values.map(d => d.duration_sec))
    return ({
      method_id,
      error_pct_error,
      error_pct_oom,
      error_pct_timeout,
      error_pct_ok,
      // error_reason: {
      //   "Memory limit exceeded": error_pct_oom,
      //   "Time limit exceeded": error_pct_timeout,
      //   "Execution error": error_pct_error,
      //   "No error": error_pct_ok
      // },
      error_reason: [error_pct_oom, error_pct_timeout, error_pct_error, error_pct_ok],
      mean_cpu_pct: mean_na_rm(values.map(d => d.cpu_pct)),
      mean_peak_memory_mb,
      mean_peak_memory_log: -Math.log10(mean_peak_memory_mb),
      mean_peak_memory_str: " " + label_memory(mean_peak_memory_mb) + " ",
      mean_disk_read_mb: mean_na_rm(values.map(d => d.disk_read_mb)),
      mean_disk_read_log: -Math.log10(mean_disk_read_mb),
      mean_disk_read_str: " " + label_memory(mean_disk_read_mb) + " ",
      mean_disk_write_mb: mean_na_rm(values.map(d => d.disk_write_mb)),
      mean_disk_write_log: -Math.log10(mean_disk_write_mb),
      mean_disk_write_str: " " + label_memory(mean_disk_write_mb) + " ",
      mean_duration_sec,
      mean_duration_log: -Math.log10(mean_duration_sec),
      mean_duration_str: " " + label_time(mean_duration_sec) + " "
    })
  })

summary_all = method_info
  .filter(d => show_con || !d.is_baseline)
  .filter(d => method_ids.includes(d.method_id))
  .map(method => {
    const method_id = method.method_id
    const method_name = method.method_name
    const mean_score = overall.find(d => d.method_id === method_id).mean_score
    const datasets = per_dataset.find(d => d.method_id === method_id)
    const metrics = per_metric.find(d => d.method_id === method_id)
    const resources_ = resources.find(d => d.method_id === method_id)
    return {method_id, method_name, mean_score, ...datasets, ...metrics, ...resources_}
  })
  .sort((a, b) => b.mean_score - a.mean_score)

// make sure the first entry contains all columns
column_info = [
  {id: "method_name", name: "Name", label: null, group: "method", geom: "text", palette: null},
  {id: "mean_score", name: "Score", group: "overall", geom: "bar", palette: "overall"},
  {id: "error_reason", name: "Error reason", group: "overall", geom: "pie", palette: "error_reason"},
  ...dataset_info
    .filter(d => dataset_ids.includes(d.dataset_id)).map(d => ({id: "dataset_" + d.dataset_id, name: d.dataset_name, group: "dataset", geom: "funkyrect", palette: "dataset"}))
    .sort((a, b) => a.name.localeCompare(b.name)),
  ...metric_info
    .filter(d => metric_ids.includes(d.metric_id)).map(d => ({id: "metric_" + d.metric_id, name: d.metric_name, group: "metric", geom: "funkyrect", palette: "metric"}))
    .sort((a, b) => a.name.localeCompare(b.name)),
  {id: "mean_cpu_pct", name: "%CPU", group: "resources", geom: "funkyrect", palette: "resources"},
  {id: "mean_peak_memory_log", name: "Peak memory", label: "mean_peak_memory_str", group: "resources", geom: "rect", palette: "resources"},
  {id: "mean_disk_read_log", name: "Disk read", label: "mean_disk_read_str", group: "resources", geom: "rect", palette: "resources"},
  {id: "mean_disk_write_log", name: "Disk write", label: "mean_disk_write_str", group: "resources", geom: "rect", palette: "resources"},
  {id: "mean_duration_log", name: "Duration", label: "mean_duration_str", group: "resources", geom: "rect", palette: "resources"}
].map(d => {
  if (d.id === "method_name") {
    return {...d, options: {width: 15, hjust: 0}}
  } else if (d.id === "is_baseline") {
    return {...d, options: {width: 1}}
  } else if (d.geom === "bar") {
    return {...d, options: {width: 4}}
  } else {
    return d
  }
})

column_groups = [
  {group: "method", palette: null, level1: ""},
  {group: "overall", palette: "overall", level1: "Overall"},
  {group: "error_reason", palette: "error_reason", level1: "Error reason"},
  {group: "dataset", palette: "dataset", level1: dataset_info.length >= 3 ? "Datasets" : ""},
  {group: "metric", palette: "metric", level1: metric_info.length >= 3 ? "Metrics" : ""},
  {group: "resources", palette: "resources", level1: "Resources"}
]

palettes = [
  {
    overall: "Greys",
    dataset: "Blues",
    metric: "Reds",
    resources: "YlOrBr",
    error_reason: {
      colors: ["#8DD3C7", "#FFFFB3", "#BEBADA", "#FFFFFF"],
      names: ["Memory limit exceeded", "Time limit exceeded", "Execution error", "No error"]
    }
  }
][0]

funkyheatmap(
    transpose_list_of_objects(summary_all),
    transpose_list_of_objects(column_info),
    [],
    transpose_list_of_objects(column_groups),
    [],
    palettes,
    {
        fontSize: 14,
        rowHeight: 26,
        rootStyle: 'max-width: none',
        colorByRank: color_by_rank,
        theme: {
            oddRowBackground: 'var(--bs-body-bg)',
            evenRowBackground: 'var(--bs-button-hover)',
            textColor: 'var(--bs-body-color)',
            strokeColor: 'var(--bs-body-color)',
            headerColor: 'var(--bs-body-color)',
            hoverColor: 'var(--bs-body-color)'
        }
    },
    scale_column
);

Figure 1: Overview of the results per method. This figures shows the mean of the scaled scores (group Overall), the mean scores per dataset (group Dataset) and the mean scores per metric (group Metric).

Display settings

viewof color_by_rank = Inputs.toggle({label: "Color by rank:", value: true})
viewof scale_column = Inputs.toggle({label: "Minmax column:", value: false})
viewof show_con = Inputs.toggle({label: "Show control methods:", value: true})

Filter datasets

viewof dataset_ids = Inputs.checkbox(
  dataset_info.filter(d => poss_dataset_ids.includes(d.dataset_id)),
  {
    keyof: d => d.dataset_name,
    valueof: d => d.dataset_id,
    value: dataset_info.map(d => d.dataset_id),
    label: "Datasets:"
  }
)

Filter methods

viewof method_ids = Inputs.checkbox(
  method_info.filter(d => poss_method_ids.includes(d.method_id)),
  {
    keyof: d => d.method_name,
    valueof: d => d.method_id,
    value: method_info.map(d => d.method_id),
    label: "Methods:"
  }
)

Filter metrics

viewof metric_ids = Inputs.checkbox(
  metric_info.filter(d => poss_metric_ids.includes(d.metric_id)),
  {
    keyof: d => d.metric_name,
    valueof: d => d.metric_id,
    value: metric_info.map(d => d.metric_id),
    label: "Metrics:"
  }
)

funkyheatmap = (await require('d3@7').then(d3 => {
  window.d3 = d3;
  window._ = _;
  return import('https://unpkg.com/funkyheatmapjs@0.2.5');
})).default;

Results

Results table of the scores per method, dataset and metric (after scaling). Use the filters to make a custom subselection of methods and datasets. The “Overall mean” dataset is the mean value across all datasets.

Dataset info

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Mouse brain atlas

Source dataset · Data source

A murine brain atlas with adjacent cell types as assumed benchmark truth, inferred from deconvolution proportion correlations using matching 10x Visium slides (see Dimitrov et al., 2022). 14249 cells x 34617 features with 23 cell type labels (Tasic et al. 2016).

Method info

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CellPhoneDB (max)

Repository · Source Code · Container · v1.0.0

CellPhoneDBv2 calculates a mean of ligand-receptor expression as a measure of interaction magnitude, along with a permutation-based p-value as a measure of specificity. Here, we use the former to prioritize interactions, subsequent to filtering according to p-value less than 0.05 (Efremova et al. 2020)

CellPhoneDB (sum)

Repository · Source Code · Container · v1.0.0

CellPhoneDBv2 calculates a mean of ligand-receptor expression as a measure of interaction magnitude, along with a permutation-based p-value as a measure of specificity. Here, we use the former to prioritize interactions, subsequent to filtering according to p-value less than 0.05 (Efremova et al. 2020)

Connectome (max)

Repository · Source Code · Container · v1.0.0

Connectome uses the product of ligand-receptor expression as a measure of magnitude, and the average of the z-transformed expression of ligand and receptor as a measure of specificity (Raredon et al. 2022)

Connectome (sum)

Repository · Source Code · Container · v1.0.0

Connectome uses the product of ligand-receptor expression as a measure of magnitude, and the average of the z-transformed expression of ligand and receptor as a measure of specificity (Raredon et al. 2022)

Log2FC (max)

Repository · Source Code · Container · v1.0.0

logFC (implemented in LIANA and inspired by iTALK) combines both expression and magnitude, and represents the average of one-versus-the-rest log2-fold change of ligand and receptor expression per cell type (Dimitrov et al. 2022)

Log2FC (sum)

Repository · Source Code · Container · v1.0.0

logFC (implemented in LIANA and inspired by iTALK) combines both expression and magnitude, and represents the average of one-versus-the-rest log2-fold change of ligand and receptor expression per cell type (Dimitrov et al. 2022)

Magnitude Rank Aggregate (max)

Repository · Source Code · Container · v1.0.0

RobustRankAggregate generates a consensus rank of all methods implemented in LIANA providing either specificity or magnitude scores (Dimitrov et al. 2022)

Magnitude Rank Aggregate (sum)

Repository · Source Code · Container · v1.0.0

RobustRankAggregate generates a consensus rank of all methods implemented in LIANA providing either specificity or magnitude scores (Dimitrov et al. 2022)

NATMI (max)

Repository · Source Code · Container · v1.0.0

NATMI uses the product of ligand-receptor expression as a measure of magnitude. As a measure of specificity, NATMI proposes specificity.edge = \frac{l}{l_s} \cdot \frac{r}{r_s}; where l and r represent the average expression of ligand and receptor per cell type, and l_s and r_s represent the sums of the average ligand and receptor expression across all cell types. We use its specificity measure, as recommended by the authors for single-context predictions (Hou et al. 2020)

NATMI (sum)

Repository · Source Code · Container · v1.0.0

NATMI uses the product of ligand-receptor expression as a measure of magnitude. As a measure of specificity, NATMI proposes specificity.edge = \frac{l}{l_s} \cdot \frac{r}{r_s}; where l and r represent the average expression of ligand and receptor per cell type, and l_s and r_s represent the sums of the average ligand and receptor expression across all cell types. We use its specificity measure, as recommended by the authors for single-context predictions (Hou et al. 2020)

SingleCellSignalR (max)

Repository · Source Code · Container · v1.0.0

SingleCellSignalR provides a magnitude score as LRscore = \frac{\sqrt{lr}}{\mu+\sqrt{lr}}; where l and r are the average ligand and receptor expression per cell type, and \mu is the mean of the expression matrix (Cabello-Aguilar et al. 2020)

SingleCellSignalR (sum)

Repository · Source Code · Container · v1.0.0

SingleCellSignalR provides a magnitude score as LRscore = \frac{\sqrt{lr}}{\mu+\sqrt{lr}}; where l and r are the average ligand and receptor expression per cell type, and \mu is the mean of the expression matrix (Cabello-Aguilar et al. 2020)

Specificity Rank Aggregate (max)

Repository · Source Code · Container · v1.0.0

RobustRankAggregate generates a consensus rank of all methods implemented in LIANA providing either specificity or magnitude scores (Dimitrov et al. 2022)

Specificity Rank Aggregate (sum)

Repository · Source Code · Container · v1.0.0

RobustRankAggregate generates a consensus rank of all methods implemented in LIANA providing either specificity or magnitude scores (Dimitrov et al. 2022)

Control method info

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Random Events

Repository · Source Code · Container · v1.0.0

Random generation of cell-cell communication events by random selection of ligand, receptor, source, target, and score (Open Problems for Single Cell Analysis Consortium 2022)

True Events

Repository · Source Code · Container · v1.0.0

Perfect prediction of cell-cell communication events from target data (Open Problems for Single Cell Analysis Consortium 2022)

Metric info

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Precision-recall AUC

Source code · Container

Area under the precision-recall curve for the binary classification task predicting interactions (Davis and Goadrich 2006).

Odds Ratio

Source code · Container

The odds ratio represents the ratio of true and false positives within a set of prioritized interactions (top ranked hits) versus the same ratio for the remainder of the interactions. Thus, in this scenario odds ratios quantify the strength of association between the ability of methods to prioritize interactions and those interactions assigned to the positive class (Bland 2000).

Quality control results

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✓ All checks succeeded!

Normalisation visualisation

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Authors

• Daniel Dimitrov (maintainer, author)

• Scott Gigante (contributor) ,

• Robrecht Cannoodt (contributor) ,

• Vishnuvasan Raghuraman (contributor)

References

Bland, J. M. 2000. “Statistics Notes: The Odds Ratio.” BMJ 320 (7247): 1468–68. https://doi.org/10.1136/bmj.320.7247.1468.

Cabello-Aguilar, Simon, Mélissa Alame, Fabien Kon-Sun-Tack, Caroline Fau, Matthieu Lacroix, and Jacques Colinge. 2020. “SingleCellSignalR: Inference of Intercellular Networks from Single-Cell Transcriptomics.” Nucleic Acids Research 48 (10): e55–55. https://doi.org/10.1093/nar/gkaa183.

Davis, Jesse, and Mark Goadrich. 2006. “The Relationship Between Precision-Recall and ROC Curves.” In Proceedings of the 23rd International Conference on Machine Learning - ICML 06. ACM Press. https://doi.org/10.1145/1143844.1143874.

Dimitrov, Daniel, Dénes Türei, Martin Garrido-Rodriguez, Paul L. Burmedi, James S. Nagai, Charlotte Boys, Ricardo O. Ramirez Flores, et al. 2022. “Comparison of Methods and Resources for Cell-Cell Communication Inference from Single-Cell RNA-Seq Data.” Nature Communications 13 (1). https://doi.org/10.1038/s41467-022-30755-0.

Efremova, Mirjana, Miquel Vento-Tormo, Sarah A. Teichmann, and Roser Vento-Tormo. 2020. “CellPhoneDB: Inferring Cellcell Communication from Combined Expression of Multi-Subunit Ligandreceptor Complexes.” Nature Protocols 15 (4): 1484–1506. https://doi.org/10.1038/s41596-020-0292-x.

Hou, Rui, Elena Denisenko, Huan Ting Ong, Jordan A. Ramilowski, and Alistair R. R. Forrest. 2020. “Predicting Cell-to-Cell Communication Networks Using NATMI.” Nature Communications 11 (1). https://doi.org/10.1038/s41467-020-18873-z.

Open Problems for Single Cell Analysis Consortium. 2022. “Open Problems.” https://openproblems.bio.

Raredon, Micha Sam Brickman, Junchen Yang, James Garritano, Meng Wang, Dan Kushnir, Jonas Christian Schupp, Taylor S. Adams, et al. 2022. “Computation and Visualization of Cellcell Signaling Topologies in Single-Cell Systems Data Using Connectome.” Scientific Reports 12 (1). https://doi.org/10.1038/s41598-022-07959-x.

Tasic, Bosiljka, Vilas Menon, Thuc Nghi Nguyen, Tae Kyung Kim, Tim Jarsky, Zizhen Yao, Boaz Levi, et al. 2016. “Adult Mouse Cortical Cell Taxonomy Revealed by Single Cell Transcriptomics.” Nature Neuroscience 19 (2): 335–46. https://doi.org/10.1038/nn.4216.