enhance_volcano — enhance_volcano • RNAseqStat

an enhance_colcano function for DEG volcano plot

enhance_volcano(
  deg_data,
  x,
  y,
  label = c("Down", "Stable", "Up"),
  label_ns = "Stable",
  palette = c("#66c2a5", "grey50", "#fc8d62"),
  cut_FC = "auto",
  cut_P = 0.05,
  top = 10,
  size = 2,
  expand = c(0.25, 0.25),
  genes_list = "top",
  highlight = NULL
)

Arguments

deg_data: a DEG data frame contains logFC and p value
x: which column is log FC
y: which column is P value
label: symbol word for groups,default is `c("Down","Stable","Up")`
label_ns: which group is the stable group
palette: color for every label
cut_FC: a numeric vector in threshold value of log FC
cut_P: threshold value of P value, can set for every cut_FC number in numeric vector format
top: a single number or a length of 2 numeric vector, if 2 numeric vector, first one is top max logFC.
size: a single number of font size
expand: if labels in plot display wrong, try increase it.
genes_list: a gene names character vectors;
highlight: a gene names character vectors; default NULL

Value

a ggplot ob

Examples

enhance_volcano(DEG_df,x = 'log2FoldChange', y = 'pvalue',
                label = c("Down","Stable","Up"), label_ns = "Stable",
                palette = c('#66c2a5', 'grey50', '#fc8d62'),
                cut_FC = "auto",cut_P = 0.05,top = 10, size = 2.0,expand = c(0.25,0.25),
                genes_list = "top", highlight = NULL)
#> Down 275 
#> Stable 24015 
#> Up 662