volcano_plot: Generate Volcano plot base on Deseq_analysis or...

In LorMe: Lightening One-Code Resolving Microbial Ecology Solution

Generate Volcano plot base on Deseq_analysis or indicator_analysis results

Description

Generate Volcano plot base on Deseq_analysis or indicator_analysis results

Usage

volcano_plot(inputframe, cutoff = NULL, aes_col = c("#FE5C5C", "#75ABDE"))

Arguments

inputframe	A data frame containing the results based on Deseq_analysis or indicator_analysis (only two group indicators)
cutoff	A numeric value specifying the fold change cutoff,should be the same as in Deseq_analysis
aes_col	A named vector of colors to be used in the plots

Value

A list of two ggplot objects, one for the fold change versus adjusted p-value plot and another for the mean abundance versus fold change or enrichment factor plot.

Author(s)

Wang Ningqi [e-mail]

Examples

###data prepration###

{
  # Load data
  data("Two_group")

  # Define color based on treatment column
  mycolor <- Two_group$configuration$treat_col

  ### DESeq analysis ###
  deseq_results <- Deseq_analysis(
    taxobj = Two_group,
    taxlevel = "Genus",
    cutoff = 1,
    control_name = "Control"
  )

  ### Or indicator analysis ###
  indicator_results <- indicator_analysis(
    taxobj = Two_group,
    taxlevel = "Genus"
  )

  # Create volcano plot for DESeq results
  volcano_plot <- volcano_plot(
    inputframe = deseq_results,
    cutoff = 1,
    aes_col = mycolor
  )
  print(volcano_plot$FC_FDR)  # Fold Change and FDR values
  print(volcano_plot$Mean_FC)  # Mean Fold Change values

  # Create volcano plot for indicator results
  volcano_plot <- volcano_plot(
    inputframe = indicator_results,
    cutoff = 1,
    aes_col = mycolor
  )
  print(volcano_plot$FC_FDR)  # Fold Change and FDR values
  print(volcano_plot$Mean_FC)  # Mean Fold Change values
}

LorMe documentation built on Sept. 13, 2024, 9:07 a.m.