composition_plot: This function returns a list where the 1st element is plot...

In Single-Cell-Genomics-Group-CNAG-CRG/SCrafty-package: R package to store useful functions to analyze single-cell data that the entire team can benefit

This function returns a list where the 1st element is plot composition representing the absolute number and proportion of a variable grouped by a feature of interest and the 2nd are the individual plots..

Description

This function returns a list where the 1st element is plot composition representing the absolute number and proportion of a variable grouped by a feature of interest and the 2nd are the individual plots..

Usage

composition_plot(
  metadata,
  x,
  grouping_vr,
  gradient_col = c("#7ab2ff", "#ffc157", "#fa5e25"),
  col_df = NULL,
  x_order = NULL,
  grouping_order = NULL,
  title = "",
  label = FALSE
)

Arguments

metadata	metadata from the Seurat object - se_obj\@meta.data
x	character string indicating the X axis - cell type annotation
grouping_vr	character string specifying the feature to group the data by - condition
gradient_col	vector of n colors indicating the color gradient to use in the proportion tile plot
col_df	data frame with variables name and color containing the name - color pair
x_order	character string vector containing the x names in the desired order
grouping_order	character string vector containing the grouping names in the desired order
title	character string indicating the plot title, by default and empty string ""
label	Logical vector indicating if we want to show proportion labels in the tile plot. By default FALSE.

Value

Composition plot

Examples

## Not run: 
library(Seurat)
library(SeuratData)
# SeuratData::InstallData(ds = "pbmcsca")
se_obj <- SeuratData::LoadData(ds = "pbmcsca")

col_df <- data.frame(
  "name" = unique([e-mail]$CellType),
  "color" = terrain.colors(10)
)

grouping_order <- c("Cytotoxic T cell", "CD4+ T cell", "CD14+ monocyte", "B cell",
             "Megakaryocyte", "CD16+ monocyte", "Natural killer cell",
             "Dendritic cell", "Plasmacytoid dendritic cell", "Unassigned")
SCrafty::composition_plot(
  metadata = [e-mail],
  x = "Method",
  grouping_vr = "CellType",
  gradient_col = rainbow(5),
  col_df = col_df,
  x_order = unique([e-mail]$Method),
  grouping_order = grouping_order,
  title = "Distribution of cells over methods",
  label = TRUE
)


## End(Not run)

Single-Cell-Genomics-Group-CNAG-CRG/SCrafty-package documentation built on Aug. 20, 2022, 9:29 a.m.