Outputs a heatmap of the MSStats results created using the log2fold changes — artmsPlotHeatmapQuant • artMS
Description: Heatmap of the Relative Quantifications (MSStats results)

# Outputs a heatmap of the MSStats results created using the log2fold changes

Source: `R/plots.R`
`artmsPlotHeatmapQuant.Rd`

Heatmap of the Relative Quantifications (MSStats results)

    artmsPlotHeatmapQuant(
      input_file,
      output_file = "quantifications_heatmap.pdf",
      species,
      labels = "*",
      cluster_cols = FALSE,
      display = "log2FC",
      lfc_lower = -2,
      lfc_upper = 2,
      whatPvalue = "adj.pvalue",
      FDR = 0.05,
      verbose = TRUE
    )

## Arguments

input_file | (char) MSstats `results.txt` file and location (or data.frame of resuts)
output_file | (char) Output file name (pdf format) and location. Default:"quantifications_heatmap.pdf"
species | (char). Specie name to be able to add the Gene name. To find out more about the supported species check `?artmsMapUniprot2Entrez`
labels | (vector) of uniprot ids if only specific labes would like to be plotted. Default: all labels
cluster_cols | (boolean) `True` or `False` to cluster columns. Default: FALSE
display | Metric to be displayed. Options: `log2fc` (default) `adj.pvalue` `pvalue`
lfc_lower | (int) Lower limit for the log2fc. Default: -2
lfc_upper | (int) Upper limit for the log2fc. Default: +2
whatPvalue | (char) `pvalue` or `adj.pvalue` (default)
FDR | (int) Upper limit false discovery rate (or pvalue). Default: 0.05
verbose | (logical) `TRUE` (default) shows function messages

## Value

(pdf or ggplot2 object) heatmap of the MSStats results using the selected metric

## Examples

    # Unfortunately, the example does not contain any significant hits
    # Use for illustration purposes
    artmsPlotHeatmapQuant(input_file = artms_data_ph_msstats_results,
                           species = "human",
                           output_file = NULL,
                           whatPvalue = "pvalue",
                           lfc_lower = -1,
                           lfc_upper = 1)
    #> >> TOTAL NUMBER OF SELECTED HITS FOR PLOTS WITH LFC BETWEEN -1 AND 1 AT 0.05 FDR:984