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

Source: R/plots.R

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