artmsPlotHeatmapQuant: Outputs a heatmap of the MSStats results created using the...
In kroganlab/artMS: Analytical R tools for Mass Spectrometry

artmsPlotHeatmapQuant

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)

kroganlab/artMS documentation built on July 7, 2023, 5:35 a.m.