heatmap_plot: Tailored heatmap plot

In andreaskapou/SeuratPipe: Packaging common Seurat analysis tasks

Tailored heatmap plot

Description

Heatmap plot showing marker genes after the clustering process. Expression levels are taken from the scaled.data slot. Current implementation is 'hard' coded: that is for heatmap column annotation, it assumes the Seurat object contains 'condition', 'sample' and 'seurat_clusters' as columns in meta.data slot.

Usage

heatmap_plot(
  seu,
  markers,
  topn_genes = 10,
  diff_cluster_pct = 0.1,
  pval_adj = 0.05,
  filename = NULL,
  col_pal = NULL,
  heatmap_downsample_cols = NULL,
  ...
)

Arguments

seu	Seurat object (required).
markers	Data frame with marker genes for each cluster. Expects a format as the output of Seurat's FindAllMarkers.
topn_genes	Top N marker genes to plot for each cluster.
diff_cluster_pct	Retain marker genes per cluster if their pct.1 - pct.2 > diff_cluster_pct, i.e. they show cluster specific expression. Set to -Inf, to ignore this additional filtering.
pval_adj	Adjusted p-value threshold to consider marker genes per cluster.
filename	Filename for saving the heatmap plot. If null, the heatmap is just plotted in device.
col_pal	Discrete colour palette to use, default is Hue palette (hue_pal) from 'scales' package.
heatmap_downsample_cols	If numberic, it will downsamples the columns of the heatmap plot, so a big specific cluster doesn't dominate the heatmap.
...	Additional parameters passed to 'pheatmap' function

Value

A ggplot2 object.

Author(s)

C.A.Kapourani [e-mail]

andreaskapou/SeuratPipe documentation built on Nov. 22, 2022, 4:16 p.m.