PlotsHumanProtCorr: PlotsHumanProtCorr

In CaronLab/MHCIatlas: Package to reproduce data analysis and further explore the data depicted by Kubiniok et al. 2021 in 'Global Analysis of the Mammalian MHC class I Immunopeptidome at the Organism-Wide Scale'.

Description

Function to visualize correlations of protein intensities and MHCI peptide counts across tissues and donors in human

Usage

PlotsHumanProtCorr(
  Human_ProtCorrelations,
  SigGene_names = NULL,
  allSigprots = TRUE,
  RankSigThreshold = 2,
  path_filename = NA,
  return_list_of_plots = TRUE
)

Arguments

Human_ProtCorrelations	List which is output object from the function MakeCorrHuman
SigGene_names	List of genes of interest, Default: NULL
allSigprots	Logical to generate plots for all genes (TRUE) or for a specified list of genes (FALSE), Default: TRUE
RankSigThreshold	Number of donors where a gene has to be found with significant correlation, Default: 2
path_filename	path and filename where a pdf file containing all plots is to be written to (optional), Default: NA
return_list_of_plots	Logical, can return a list with plots for each gene, Default: TRUE

Value

list of plots for each gene as ggplot2 object

See Also

ggplot,aes,geom_smooth,geom_point,labs,scale_colour_brewer,theme,margin stat_poly_eq geom_label_repel

Examples

## Not run: 
plots_h<-PlotsHumanProtCorr(corrs_h,SigGene_names=c('HLA-B'),
allSigprots=F,path_filename='~/HLAB.pdf')

## End(Not run)

CaronLab/MHCIatlas documentation built on March 10, 2021, 12:38 a.m.