sample_correlation: sample_correlation Function

In aifimmunology/PALMO: Identify Intra and Inter-Donor Variations in Bulk or Single Cell Longitudinal Dataset

sample_correlation Function

Description

This function allows to perform sample correlation (by group like celltype, or by donor).

Usage

sample_correlation(
  data_object,
  cor_method = "spearman",
  group_by = NULL,
  col_break = NULL,
  col_max = 1,
  cluster_rows = FALSE,
  cluster_columns = FALSE,
  column_names_fontsize = 4,
  row_names_fontsize = 4,
  row_title_fontsize = 6,
  column_title_fontsize = 6,
  plotHeight = 20,
  fileName = NULL,
  filePATH = NULL
)

Arguments

data_object	Input PALMO S4 object. It contains annotation information and expression data from Bulk or single cell data.
cor_method	(Optional) Correlation method 'pearson' or 'spearman'. Default is 'spearman'
group_by	Cluster correlation heat plot by 'donor' or 'group'
col_break	Value between 0 and 1
col_max	Maximum color limit (Default 1)
cluster_rows	ComplexHeatmap cluster rows, Default FALSE
cluster_columns	ComplexHeatmap cluster columns, Default FALSE
column_names_fontsize	Font size of the column names, Default 4
row_names_fontsize	Font size of the row names, Default 4
row_title_fontsize	Font size of the row title, Default 6
column_title_fontsize	Font size of the column title, Default 6
plotHeight	Height of the plot in inch, Default 20 in
fileName	User-defined file name, Default outputFile
filePATH	User-defined output directory PATH Default, current directory

Value

PALMO object with correlation cor_res dataframe

Examples

## Not run: 
palmo_obj <- sample_correlation(data_object=palmo_obj, group_by="Time")

## End(Not run)

aifimmunology/PALMO documentation built on Oct. 21, 2022, 7:39 p.m.