Plot the gene set enrichment results with ComplexHeatmap

This function takes the output of gene_set_enrichment() and creates a ComplexHeatmap visualization of the results. Fill of the heatmap represents the -log10(p-val), Odds-ratios are printed for test that pass specified significance threshold ORcut.

gene_set_enrichment_plot(
  enrichment,
  xlabs = unique(enrichment$ID),
  PThresh = 12,
  ORcut = 3,
  enrichOnly = FALSE,
  mypal = c("white", RColorBrewer::brewer.pal(9, "YlOrRd")),
  plot_SetSize_bar = FALSE,
  gene_list_length = NULL,
  model_sig_length = NULL,
  model_colors = NULL,
  ...
)

Arguments

enrichment: The output of gene_set_enrichment().
xlabs: A vector of names in the same order and length as unique(enrichment$ID).
PThresh: A numeric(1) specifying the P-value threshold for the maximum value in the -log10(p) scale.
ORcut: A numeric(1) specifying the P-value threshold for the minimum value in the -log10(p) scale for printing the odds ratio values in the cells of the resulting plot. Defaults to 3 or p-val < 0.001.
enrichOnly: A logical(1) indicating whether to show only odds ratio values greater than 1.
mypal: A character vector with the color palette to use. Colors will be in order from 0 to lowest P-val max(-log(enrichment$Pval)). Defaults to white, yellow, red pallet.
plot_SetSize_bar: A logical(1) indicating whether to plot SetSize from enrichment as an anno_barplot at the top of the heatmap.
gene_list_length: Optional named numeric vector indicating the length of the gene_list used to calculate enrichment, if included and plot_setSize_bar = TRUE then the top anno_barplot will show the SetSize and the difference from the length of the input gene_list.
model_sig_length: Optional named numeric vector indicating the number of significant genes in modeling_results used to calculate enrichment. If included anno_barplot will be added to rows.
model_colors: named character vector of colors. It adds colors to row annotations.
...: Additional parameters passed to ComplexHeatmap::Heatmap().

Value

A (Heatmap-class) visualizing the gene set enrichment odds ratio and p-value results.

Details

Includes functionality to plot the size of the input gene sets as barplot annotations.

Check https://github.com/LieberInstitute/HumanPilot/blob/master/Analysis/Layer_Guesses/check_clinical_gene_sets.R to see a full script from where this family of functions is derived from.

Author

Andrew E Jaffe, Leonardo Collado-Torres, Louise Huuki-Myers

Examples


## Read in the SFARI gene sets included in the package
asd_sfari <- utils::read.csv(
    system.file(
        "extdata",
        "SFARI-Gene_genes_01-03-2020release_02-04-2020export.csv",
        package = "spatialLIBD"
    ),
    as.is = TRUE
)

## Format them appropriately
asd_safari_geneList <- list(
    Gene_SFARI_all = asd_sfari$ensembl.id,
    Gene_SFARI_high = asd_sfari$ensembl.id[asd_sfari$gene.score < 3],
    Gene_SFARI_syndromic = asd_sfari$ensembl.id[asd_sfari$syndromic == 1]
)

## Obtain the necessary data
if (!exists("modeling_results")) {
    modeling_results <- fetch_data(type = "modeling_results")
}
#> 2024-12-16 21:50:57.796293 loading file /github/home/.cache/R/BiocFileCache/5db39a09009_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1

## Compute the gene set enrichment results
asd_sfari_enrichment <- gene_set_enrichment(
    gene_list = asd_safari_geneList,
    modeling_results = modeling_results,
    model_type = "enrichment"
)

## Visualize the gene set enrichment results

## Default plot
gene_set_enrichment_plot(
    enrichment = asd_sfari_enrichment
)


## Use a custom green color palette & use shorter gene set names
## (x-axis labels)
gene_set_enrichment_plot(
    asd_sfari_enrichment,
    xlabs = gsub(".*_", "", unique(asd_sfari_enrichment$ID)),
    mypal = c("white", RColorBrewer::brewer.pal(9, "BuGn"))
)


## Add bar plot annotations for SetSize of model genes in the gene_lists
gene_set_enrichment_plot(
    asd_sfari_enrichment,
    xlabs = gsub(".*_", "", unique(asd_sfari_enrichment$ID)),
    plot_SetSize_bar = TRUE
)


## Add stacked bar plot annotations showing SetSize and difference from the
## length of the input gene_list
gene_set_enrichment_plot(
    asd_sfari_enrichment,
    xlabs = gsub(".*_", "", unique(asd_sfari_enrichment$ID)),
    plot_SetSize_bar = TRUE,
    gene_list_length = lapply(asd_safari_geneList, length)
)


## add bar plot annotations for number of enriched genes from layers
if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer")
#> 2024-12-16 21:51:02.513146 loading file /github/home/.cache/R/BiocFileCache/5db16a912b9_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
sig_genes <- sig_genes_extract(
    modeling_results = modeling_results,
    model = "enrichment",
    sce_layer = sce_layer,
    n = nrow(sce_layer)
)

sig_genes <- sig_genes[sig_genes$fdr < 0.1, ]
n_sig_model <- as.list(table(sig_genes$test))

## add barplot with n significant genes from modeling
gene_set_enrichment_plot(
    asd_sfari_enrichment,
    xlabs = gsub(".*_", "", unique(asd_sfari_enrichment$ID)),
    plot_SetSize_bar = TRUE,
    model_sig_length = n_sig_model
)


## add color annotations
gene_set_enrichment_plot(
    asd_sfari_enrichment,
    xlabs = gsub(".*_", "", unique(asd_sfari_enrichment$ID)),
    plot_SetSize_bar = TRUE,
    model_colors = libd_layer_colors
)


## add barplot with n significant genes from modeling filled with model color
gene_set_enrichment_plot(
    asd_sfari_enrichment,
    xlabs = gsub(".*_", "", unique(asd_sfari_enrichment$ID)),
    plot_SetSize_bar = TRUE,
    model_sig_length = n_sig_model,
    model_colors = libd_layer_colors
)

Arguments

Value

Details

See also

Author

Examples