seurat_volcano: Deseq2 style Volcano plot

In Yutong441/TBdev: Infer a Trophoblast Developmental Trajectory

Description

Deseq2 style Volcano plot

Usage

seurat_volcano(
  markers,
  group1,
  group2,
  group1_col = "group",
  group2_col = "compare_group",
  label_genes = NULL,
  weighting = "logFC",
  pval = "padj",
  gene = "feature",
  weight_thres = 0.25,
  show_gene_num = 30,
  logy = T,
  AP = NULL,
  ...
)

Arguments

markers	a dataframe, result generated from find_DE_genes
group1	comparison group1
group2	comparison group2
group1_col	a column in markers where group1 information is stored
group2_col	a column in markers where group2 information is stored
label_genes	which genes to show in the volcano plot
weighting	the x axis, i.e. log fold change
pval	the p value for the y axis
gene	where the gene names are stored
weight_thres	above which value in weighting are the points colored according to their comparison groups
AP	aesthetic parameter for controlling the plot
...	arguments for enrich_arrow, including nudge_x, nudge_y and band_thickness, length_ratio. For description of their roles, see enrich_bar

Value

a ggplot object

Yutong441/TBdev documentation built on Dec. 18, 2021, 8:22 p.m.