Generate heatmap of DE genes from multiple treatments This is the function to generate a heatmap of DE genes from running compute_multi_DE that shared by more than one treatment group. There are a few options available to help you to extract shared DE genes.

Usage

plot_multi_de(
  data = NULL,
  group_by = NULL,
  value = NULL,
  p_value_cutoff = 0.01,
  direction = "both",
  n_genes = 10,
  control = "DMSO_0",
  by = "fc",
  gene_list = NULL
)

Arguments

data: A tidyseurat object merged with metadata. Must contain columns "Well_ID", "Row", "Column".
group_by: A column that specifies the treatment group in the input data
value: To use logCPM, log2FC or metric in the heatmap
p_value_cutoff: Cutoff for adjusted p-value (column p_value_adj), default 0.01
direction: Direction to select up or down regulated genes or in both directions
n_genes: Top n genes to be extracted from each treatment comparison
control: The control group to be included in the final heatmap, usually DMSO_0
by: Extract top n genes by either absolute fold change or by adjusted p-value
gene_list: External list of genes to plot the heatmap on

Value

a pheatmap object

Examples

data("mini_mac")
plot_multi_de(mini_mac,group_by = "combined_id", 
             value = "log2fC", p_value_cutoff = 0.01, direction="up", 
             n_genes = 10, control = "DMSO_0", by="fc")