artmsPlotHeatmapQuant {artMS} | R Documentation

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

### Description

Heatmap of the Relative Quantifications (MSStats results)

### Usage

    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)

[Package artMS version 1.10.2 Index]