cellscatterplots: Draw scatter plots to compare two sets of cell content values

In yuabrahamliu/scDeconv: scDeconv is an R Package to Deconvolve Bulk DNA Methylation Data with scRNA-seq Data in a Multi-omics Manner.

Draw scatter plots to compare two sets of cell content values

Description

Draw scatter plots to compare two sets of cell content values and compare two sets of cell-cell correlation values. For each cell type, its scatter plot accounts for one facet of all the plots.

Usage

cellscatterplots(
  dat1,
  dat2,
  title = NULL,
  colorful = TRUE,
  corcmp = TRUE,
  usePCC = FALSE,
  xtitle = "RNA cell contents",
  ytitle = "Methylation cell contents",
  annotextsize = 6,
  textsize = 13,
  titlesize = 15,
  face = "bold",
  dotsize = 1
)

Arguments

dat1	A data frame or matrix recording the sample cell contents in the first dataset. Each column is a cell type and each row is a sample. The column names are the cell type names and the row names are the sample IDs.
dat2	A data frame or matrix recording the cell contents for the same samples in the second dataset. Each column is a cell type and each row is a sample. The column names are the cell type names and the row names are the sample IDs.
title	A string to define the prefixes of the plot titles, can also be set as NULL.
colorful	A logical value indicating whether the dots in the scatter plots should be rainbow colored to indicate their density or not. Default is TRUE. This parameter only works when the dot number in the plot is more than 50, otherwise, all the dots will be colored as blue.
corcmp	A logical value indicating whether a scatter plot comparing the cell-cell correlation in the 2 datasets should be drawn or not. The default value is TRUE.
usePCC	If this value is TRUE, the Pearson correlation coefficient between the cell contents will be labeled in the plot. If FALSE, the R square value will be labeled instead. Default is FALSE.
xtitle	The title of the x-axes of the scatter plots. Default is "RNA cell contents".
ytitle	Title of the y-axes. Default is "Methylation cell contents".
annotextsize	A number used to define the font size of the annotation labels in the scatter plot. Default is 6.
textsize	A number to define the base font size for the plots, except the plot title size, axis title size, and the annotation label size, which are defined by codetitlesize and annotextsize. The default value is 13.
titlesize	A number to define the size for the plot and axis titles, and the default value is 15.
face	A string to define whether the text in the plot should be bold or plain. Default is "bold".
dotsize	A number to define the dot size in the scatter plots. Default is 1.

Value

Generate a scatter plot to compare the cell contents for the same samples recorded by two datasets. For each cell type, a facet will be made for its plot. If the parameter corcmp is set as TRUE, an additional scatter plot comparing the cell-cell correlation between the two datasets will also be drawn.

yuabrahamliu/scDeconv documentation built on March 28, 2024, 3:15 p.m.