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Plot Candidate Targets and Effect Sizes

Source: R/plot_candidates.R
plot_candidates.Rd

plot_candidates() visualizes effect sizes (log2 foldchange) along with Wald-type confidence intervals for specific candidate proteins or literature-nominated validation targets. Candidates can optionally be categorized and colored by validation status.

Usage

plot_candidates(
  data = NULL,
  ...,
  candidates = NULL,
  proteins = NULL,
  labels_column = "gene_name",
  status = NULL,
  status_column = NULL,
  confidence = 0.95,
  log2fc_column = "log2_foldchange",
  significance_column = "adj_p_value",
  significance_max = 0.05,
  show_title = TRUE,
  tag = NULL,
  destination = "plot",
  height = 6,
  width = 8,
  path = NULL
)

plot_forest(...)

Arguments

data

a tidyproteomics data object (or an exported expression table)

...

passthrough ggplot2::ggsave arguments.

candidates

a character vector of identifiers or gene names to include in the plot. If NULL, defaults to proteins or the top 15 candidates ranked by statistical significance and effect size.

proteins

alias for candidates for backward compatibility.

labels_column

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

status

an optional named character vector of validation status tags corresponding to gene/protein identifiers (e.g. c(HERPUD1 = "Validated", RACGAP1 = "Empirical change")).

status_column

an optional column name in the expression table containing status annotations.

confidence

numeric confidence level for intervals. Default is 0.95 (95% CI).

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.

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_candidates(
    knockdown/control,
    candidates = c("RPL26", "RPS27A", "CKS2"),
    labels_column = "gene_name"
  )
#> ℹ .. expression::t_test testing knockdown / control
#> ✔ .. expression::t_test testing knockdown / control [3.2s]
#>