PlotTopGenesPerCluster: Plot Top N Differentially Expressed Genes Per Cluster

In vertesy/Seurat.utils: Seurat.utils - utility functions for Seurat

Plot Top N Differentially Expressed Genes Per Cluster

Description

Visualizes the top N differentially expressed (DE) genes for each cluster within a specified clustering resolution of a Seurat object, facilitating the exploration of gene expression patterns across clusters.

Usage

PlotTopGenesPerCluster(
  obj = combined.obj,
  cl_res = GetClusteringRuns()[1],
  nrGenes = p$n.markers,
  order.by = c("combined.score", "avg_log2FC", "p_val_adj")[1],
  df_markers = obj@misc$df.markers[[paste0("res.", cl_res)]],
  filt_coding_genes = TRUE,
  ...
)

Arguments

obj	Seurat object containing single-cell RNA-seq data and clustering information; Default: combined.obj.
cl_res	Cluster resolution used to identify distinct clusters for analysis; Default: res.
nrGenes	Number of top DE genes to display for each cluster; Default: GetClusteringRuns()1.
order.by	Criteria for ranking DE genes within clusters; Default: "combined.score".
df_markers	Data frame or list of DE genes across clusters. If not provided, attempts to retrieve from obj@misc$df.markers[[paste0("res.", cl_res)]]; Default: calculated based on cl_res.
filt_coding_genes	Logical indicating whether to filter out non-coding genes; Default: TRUE.

Examples

## Not run: 
if (interactive()) {
  PlotTopGenesPerCluster(obj = combined.obj, cl_res = 0.5, nrGenes = 10)
}

## End(Not run)

vertesy/Seurat.utils documentation built on Dec. 4, 2024, 5:20 p.m.