Runs correlation analysis pipeline

correlation_analysis(
  main_dataset,
  SCEs,
  sampleIDs,
  celltypeIDs,
  celltype_correspondence,
  pvals = c(0.05, 0.025, 0.01, 0.001, 1e-04),
  dataset_names = "placeholder",
  alphaval = 0.25,
  N_randperms = 5,
  N_subsets = 5,
  sex_DEGs = FALSE,
  fontsize_yaxislabels = 12,
  fontsize_yaxisticks = 9,
  fontsize_title = 14,
  fontsize_legendlabels = 9,
  fontsize_legendtitle = 9,
  fontsize_facet_labels = 9,
  output_path = getwd()
)

Arguments

main_dataset: name of the dataset used to select significant DEGs from (specified as a string, name as in dataset_names)
SCEs: list of the input data (elements should be SCE objects)
sampleIDs: list or vector of sample IDs (in order of SCEs)
celltypeIDs: list or vector of cell type IDs (in order of SCEs)
celltype_correspondence: list of different names specifying each cell type
pvals: list of p-value cut-offs which will be used to select DEGs
dataset_names: names of the datasets as they appear in the correlation plot (in order of SCEs)
alphaval: (alpha) transparency of the non-mean boxplots
N_randperms: number of random permutations of the dataset used to select significant DEGs from
N_subsets: number of pairs of random subsets of the dataset used to select significant DEGs from
sex_DEGs: If TRUE, only keep genes present on sex chromosmomes. Queries hspanies gene Ensembl dataset.
fontsize_yaxislabels: font size for axis labels in plot
fontsize_yaxisticks: font size for axis tick labels in plot
fontsize_title: font size for plot title
fontsize_legendlabels: font size for legend labels in plot
fontsize_legendtitle: font size for legend title in plot
fontsize_facet_labels: font size for facet labels
output_path: base path in which outputs will be stored Saves all plots and DGE analysis outputs in the appropriate directories

Runs correlation analysis pipeline

Arguments

Examples