get_cor: Calculate and Visualize Correlation between Two Variables

In IOBR/IOBR: Immune Oncology Biological Research

Calculate and Visualize Correlation between Two Variables

Description

The "get_cor" function calculates and visualizes the correlation between two variables in a dataset. It provides options to scale the data, handle missing values, and incorporate additional data. The function supports various correlation methods and can display the correlation result. It generates a correlation plot with optional subtypes or categories, including a regression line. The plot can be customized with color palettes, labels, and titles. Additionally, the function allows saving the plot and data for further analysis.

Usage

get_cor(
  eset,
  pdata = NULL,
  is.matrix = FALSE,
  id_eset = "ID",
  id_pdata = "ID",
  var1,
  var2,
  scale = TRUE,
  subtype = NULL,
  na.subtype.rm = FALSE,
  color_subtype = NULL,
  palette = "jama",
  index = NULL,
  method = "spearman",
  show_cor_result = T,
  col_line = NULL,
  id = "NULL",
  show_lebel = FALSE,
  point_size = 4,
  title = NULL,
  alpha = 0.5,
  title_size = 1.5,
  text_size = 10,
  axis_angle = 0,
  hjust = 0,
  show_plot = TRUE,
  fig.format = "png",
  fig.width = 7,
  fig.height = 7.3,
  path = NULL,
  save_plot = FALSE,
  add.hdr.line = FALSE
)

Arguments

eset	A dataset containing the variables of interest.
pdata	An optional data frame providing additional data for the analysis. Default is NULL.
is.matrix	Whether the eset is a matrix data with feature as row names
id_eset	The column name in eset that contains unique identifiers. Default is "ID".
id_pdata	The column name in pdata that contains unique identifiers. Default is "ID".
var1	The name of the first variable to analyze.
var2	The name of the second variable to analyze.
scale	Whether to scale the data. Default is TRUE.
subtype	An optional variable that represents subtypes/categories in the analysis. Default is NULL.
na.subtype.rm	Whether to remove NA values in the subtype variable. Default is FALSE.
color_subtype	The color palette for the subtypes/categories. Default is NULL.
palette	The name of the color palette. Default is "jama".
index	The index of the plot. Default is NULL.
method	The correlation method to use. Default is "spearman".
show_cor_result	Whether to print the correlation result. Default is TRUE.
col_line	The color of the line in the correlation plot. Default is NULL.
id	The ID column name to use for labeling points on the plot. Default is "NULL".
show_lebel	Whether to show labels on the plot. Default is FALSE.
point_size	The size of the points on the plot. Default is 4.
title	The title of the plot. Default is NULL.
alpha	The transparency level of points on the plot. Default is 0.7.
title_size	The size of the title on the plot. Default is 2.
text_size	The size of the text on the plot. Default is 15.
axis_angle	The rotation angle of the axes labels on the plot. Default is 0.
hjust	The horizontal justification of the axes labels on the plot. Default is 0.
show_plot	Whether to display the plot. Default is TRUE.
fig.format	The format of the saved figure. Default is "png".
fig.width	The width of the saved figure. Default is 7.
fig.height	The height of the saved figure. Default is 7.3.
path	The path where the figure will be saved. Default is NULL.
save_plot	Whether to save the plot as a file. Default is FALSE.
add.hdr.line	add.hdr.line

Author(s)

Dongqiang Zeng

Examples

data(eset_tme_stad, package = "IOBR")
get_cor(eset = eset_tme_stad, is.matrix = TRUE, var1 = "GZMB", var2 = "CD274")

IOBR/IOBR documentation built on May 5, 2024, 2:34 p.m.