scPagwas_Visualization: scPagwas_Visualization

In dengchunyu/scPagwas: A pathway-based polygenic integration method for inferring disease-associated individual cells in single cell sequencing data

scPagwas_Visualization

Description

Visualize the scPagwas score in Umap and Tsne.

Usage

scPagwas_Visualization(
  Single_data = NULL,
  p_thre = 0.05,
  output.dirs = "scPagwastest_output",
  FigureType = "tsne",
  width = 7,
  height = 7,
  title = "",
  lowColor = "#000957",
  highColor = "#EBE645",
  size = 0.5,
  do_plot = TRUE
)

Arguments

Single_data	Single_data in seruat format ,the save with scPagwas_main(), you'd better to run reduction of UMAP AND TSNE
p_thre	(numeric),default is 0.1, Threshold for pecent(<1) of Positive cells for level of scPagwas_score.
output.dirs	(character)default is NULL.the file folder name for save the figures.NULL means no folder is created, no pdf figure output.
FigureType	(character)"tsne" or "umap
width	(numeric)Figure width
height	(numeric)Figure height
title	(character)Figure title
lowColor	(character)Color for low scPagwas score
highColor	(character)Color for high scPagwas score
size	(numeric)size for scatters
do_plot	Whether to plot, logical

Value

figures for TRS score, gPas score,and p value reduction plot

Author(s)

Chunyu Deng

Examples

load(system.file("extdata", "Pagwas_data.RData", package = "scPagwas"))
scPagwas_Visualization(
  Single_data = Pagwas_data,
  p_thre = 0.05,
  FigureType = "umap",
  width = 7,
  height = 7,
  lowColor = "white",
  highColor = "red",
  output.dirs = "figure",
  size = 0.5,
  do_plot = TRUE
)

dengchunyu/scPagwas documentation built on Nov. 29, 2024, 2:53 p.m.