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Plot Biological Signatures or Program Dichotomies

Source: R/plot_signatures.R
plot_signatures.Rd

plot_signatures() visualizes directional expression shifts across distinct biological modules, pathways, or opposing signatures (e.g., comparing upregulated quality control machinery against downregulated cell-cycle/growth machinery) as a faceted, diverging lollipop or bar chart.

Usage

plot_signatures(
  data = NULL,
  ...,
  signatures = NULL,
  programs = NULL,
  set_a = NULL,
  set_b = NULL,
  label_a = "Signature A",
  label_b = "Signature B",
  labels_column = "gene_name",
  log2fc_column = "log2_foldchange",
  significance_column = "adj_p_value",
  significance_max = 0.05,
  plot_type = c("lollipop", "bar"),
  show_title = TRUE,
  tag = NULL,
  destination = "plot",
  height = 6,
  width = 8,
  path = NULL
)

plot_programs(...)

Arguments

data

a tidyproteomics data object (or an exported expression table)

...

two sample comparison expression (e.g. knockdown/control)

signatures

a named list of character vectors of identifiers/gene names representing distinct biological signatures or programs (e.g. list("UPR" = c(...), "CellCycle" = c(...))).

programs

alias for signatures for backward compatibility.

set_a

optional convenience parameter for the first program gene set (used if signatures is NULL).

set_b

optional convenience parameter for the second program gene set (used if signatures is NULL).

label_a

character label for set_a. Default is "Signature A".

label_b

character label for set_b. Default is "Signature B".

labels_column

a character defining the column name for feature labeling. Default is "gene_name".

log2fc_column

a character defining the column name of log2 foldchange values. Default is "log2_foldchange".

significance_column

a character defining the column name of significance values. Default is "adj_p_value".

significance_max

a numeric defining the significance threshold. Default is 0.05.

plot_type

character defining geometry type, either "lollipop" (default) or "bar".

show_title

boolean or character string for plot title. Default is TRUE.

tag

optional character string to append to the plot file name.

destination

character string indicating output type: "plot", "save", "png", "svg", "tiff", "jpeg". Default is "plot".

height

numeric plot height in inches. Default is 6.

width

numeric plot width in inches. Default is 8.

path

optional path to save destination plot.

Value

a ggplot2 object or tidyproteomics data object depending on destination.

Examples

library(dplyr, warn.conflicts = FALSE)
library(tidyproteomics)

hela_proteins %>%
  expression(knockdown/control) %>%
  plot_signatures(
    knockdown/control,
    signatures = list(
      "Ribosomal" = c("RPL26", "RPS27A"),
      "Cell Cycle" = c("CKS2", "RACGAP1")
    ),
    labels_column = "gene_name"
  )
#> ℹ .. expression::t_test testing knockdown / control
#> ✔ .. expression::t_test testing knockdown / control [3.3s]
#>