Outputs a heatmap of the MSStats results created using the log2fold
changes — artmsPlotHeatmapQuant (original) (raw)
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
