Title — prot_to_map • VisomX

Title

Usage

prot_to_map(
  se,
  protein_set = NULL,
  col.id = "ID",
  select.id = "Accession",
  pfx = NULL,
  imp_fun = c("man", "bpca", "knn", "QRILC", "MLE", "MinDet", "MinProb", "min", "zero",
    "mixed", "nbavg", "SampMin"),
  q = 0.01,
  type = c("contrast", "centered"),
  condition = NULL,
  contrast = NULL,
  template = NULL,
  RSD_thresh = 0.5,
  p_thresh = 1,
  indicate_nonsig = c("gray", "dashed"),
  result = NULL,
  pal = "RdYlBu",
  legend_min = NULL,
  legend_max = NULL,
  title = "",
  export = TRUE,
  inkscape_path = "C:/Program Files/Inkscape/bin/inkscape.exe",
  export_dpi = 300,
  export_width = 2281,
  export_height = 2166
)

Arguments

se: SummarizedExperiment object, proteomics data parsed with prot.read_data.
protein_set: Data frame containing a list of proteins to be plotted. The provided names in column must match the entries in the column provided as col.id as well as the IDs of objects in the map template.
col.id: (Character) Column name of the protein identifier in the SummarizedExperiment object.
select.id: Column name of the protein identifier in the protein_set data frame.
pfx: Prefix of the protein identifiers to be plotted. all protein objects in the template map should have a common prefix (e.g., 'prot_')
imp_fun: (Character string) Function used for data imputation. "SampMin", "man", "bpca", "knn", "QRILC", "MLE", "MinDet", "MinProb", "min", "zero", "mixed", or "nbavg". See (prot.impute) for details.
q: (Numeric) q value for imputing missing values with method imp_fun = 'MinProb'.
type: (Character string) Type of analysis to perform. "contrast" (provide a specific contrast in the contrast argument to plot log2-fold change values) or "centered" (provide a single condition as condition to plot centered abundances in that condition).
condition: Condition to be displayed if type = "centered".
contrast: Tested contrast if type = "contrast" in the format "A_vs_B".
template: Path to the SVG map template.
p_thresh: (adjusted) p-value threshold.
result: Name of the output files.
pal: Brewer color palette used for protein squares.
legend_min: Lower limit of the color legend.
legend_max: Upper limit of the color legend.
title: (Character string) Title shown above the map
export: (Logical) A logical value indicating whether to export the plot as a PNG and PDF file.
inkscape_path: The local path to the 'inkscape.exe' file. Required if export = TRUE.
export_dpi: The dpi of the exported PNG and PDF file.
export_width: The width of the exported PNG and PDF file. The width of the template SVG can be inspected after opening it in InkScape.
export_height: The height of the exported PNG and PDF file. The height of the template SVG can be inspected after opening it in InkScape.
RSD_threshRelative: standard deviation threshold.

Value

A metabolic map with protein objects colored according to their abundance or log2 fold changes in a given contrast.