ThreeGroupQuadDiff

For the Beginning

Note: markers_df_hhc & markers_df_hth are dataframes from the Seurat::FindMarkers function.

Important: Please ensure that you execute Seurat::FindMarkers in the proper sequence. In Seurat::FindMarkers, the group specified by ident.1 is treated as the test group, while ident.2 is treated as the reference group.

For example, the disease progression follows the order: HC → HIV → HIV/MTB.

markers_df_hth <- Seurat::FindMarkers(object = seurat_obj, ident.1 = "HIV_MTB", ident.2 = "HIV", assay = "RNA")
markers_df_hhc <- Seurat::FindMarkers(object = seurat_obj, ident.1 = "HIV", ident.2 = "HC", assay = "RNA")

The test dataset and corresponding script are located in ./data/*.rds and ./sample_data.R, respectively. Simply running sample_data.R will reproduce the exact plot shown in this repository.

Main Executable Lines

Load the functions

source("define_functions.R")

Step 1: Select the common features of the two datasets.

markers_df_common <- common_de_marker_selection(
  de_list_1 = markers_df_hhc,
  de_list_2 = markers_df_hth,
  suffix_list = c("_hhc", "_hth"),
  xtitle = "LogFC (HIV vs HC)",
  ytitle = "LogFC (HIV_MTB vs HIV)",
  plot_title = "Common Gene LogFC Distribution among Three Groups"
)
print(markers_df_common$plot)

Step 2: Convert the combined list.

mart <- biomaRt::useMart("ensembl", dataset = "hsapiens_gene_ensembl")
converted_common_markers <- common_de_geneid_converter(
  common_de_list = markers_df_common$common_markers, mart = mart
)

Step 3: Enrich the common list using databases.

common_enrich <- common_markers_enrichment(converted_common_markers)

Hint: You might consider integrating additional databases at this stage, such as REACTOME and WikiPathways, among others.

Step 4: Select the common features of the two datasets.

p1 <- common_plot_kegg_results(
  common_enrich,
  hjust = 1.7,
  title = "KEGG for CD4 Naive in four quadrants"
)
print(p1)

Suggest Citations

print("Please consider cite the packages 'clusterProfiler' and 'biomaRt' used in this repository.")