manhattan: Manhattan Plot Generator

In LorMe: Lightening One-Code Resolving Microbial Ecology Solution

Manhattan Plot Generator

Description

Generate Manhattan Plot base on Deseq_analysis or indicator_analysis results

Usage

manhattan(
  inputframe,
  taxlevel = "Phylum",
  control_name,
  mode = "all",
  top_n = NULL,
  palette = "Set1",
  select_tax = NULL,
  rmprefix = NULL
)

Arguments

inputframe	A data frame generated from Deseq_analysis or indicator_analysis
taxlevel	Taxonomy levels used for visualization.Must be one of c("Domain","Phylum","Class","Order","Family","Genus","Species","Base").Default:NULL.
control_name	Character. The name of the control group for the comparison.
mode	The mode for selecting which taxa to plot: "all" for all taxa, "most" for the top N taxa, and "select" for specific taxa selection
top_n	The number of top taxa to plot when mode is set to "most"
palette	Character. Palette for visualization,default:"Set1".Optional palette same as 'RColorBrewer'. "Plan1" to "Plan10" were also optional,see in color_scheme
select_tax	A vector of taxa to be selected for plotting when mode is "select".
rmprefix	A string prefix to be removed from the taxonomic annotation.Default:NULL.

Value

a list containing the Manhattan plot, circular Manhattan plot, source data, and color assignments

Examples

{
  # Data preparation
  data("Two_group")

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

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

  # Show all with Manhattan plot
    manhattan_object <- manhattan(
      inputframe = deseq_results,
      taxlevel = "Phylum",
      control_name = "Control"
    )
    print(manhattan_object$manhattan)  # Tradition Manhattan plot
    print(manhattan_object$manhattan_circle)  # Circular Manhattan plot
    print(manhattan_object$sourcedata)  # Source data for plot
    print(manhattan_object$aes_color)  # Aesthetic color for plot

  # Top 8 Phyla with most taxon
    manhattan_object <- manhattan(
      inputframe = indicator_results,
      taxlevel = "Phylum",
      control_name = "Control",
      mode = "most",
      top_n = 8,
      palette = "Set1"
    )
    print(manhattan_object$manhattan)

  # Specific phyla
  # Top nine dominant phyla
    community <- community_plot(
      taxobj = Two_group,
      taxlevel = "Phylum",
      n = 9,
      palette = "Paired",
      rmprefix = "p__"
    )

    manhattan_object <- manhattan(
      inputframe = indicator_results,
      taxlevel = "Phylum",
      control_name = "Control",
      mode = "select",
      palette = community$filled_color,
      select_tax = names(community$filled_color),
      rmprefix = "p__"
    )
    print(manhattan_object$manhattan)
    print(manhattan_object$manhattan_circle)
}

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