PALMO (version 0.1.2)

sample_correlation: 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
)

Value

PALMO object with correlation cor_res dataframe

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

Examples

if (FALSE) {
palmo_obj <- sample_correlation(data_object=palmo_obj, group_by="Time")
}