enhance_volcano: enhance_volcano

In xiayh17/RNAseqStat: A Pipeline to Process RNAseq Data

enhance_volcano

Description

an enhance_colcano function for DEG volcano plot

Usage

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)

xiayh17/RNAseqStat documentation built on June 16, 2022, 11:51 a.m.