plot_vln_Corgenes: plot_vln_Corgenes

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

plot_vln_Corgenes

Description

Make grid of violin plots Thanks to the SCOPfunctions package https://github.com/CBMR-Single-Cell-Omics-Platform/SCOPfunctions/blob/main/R/plot.R

produce a n_celltype * n_genes grid of violin plots

Usage

plot_vln_Corgenes(
  seurat_obj,
  assay,
  slot,
  var_group,
  vec_features,
  vec_group_colors = NULL,
  f_color = grDevices::colorRampPalette(RColorBrewer::brewer.pal(n = 11, name =
    "RdYlBu")),
  flip = T,
  do_plot = FALSE,
  pt.size = 0,
  feature_fontface = "bold.italic",
  fontsize_axistext_x = 12,
  fontsize_axistext_y = 12,
  aspect.ratio = NULL,
  figurenames = NULL,
  width = 7,
  height = 7
)

Arguments

seurat_obj	Seurat object (Seurat ^3.0)
assay	seurat_obj assay to use
slot	seurat_obj slot to use
var_group	the group variable, character
vec_features	a vector of features to plot in the violin plot
vec_group_colors	a vector of colors, named by corresponding group. Length must match number of groups. Character
f_color	if vec_group_colors is not provided, the user may instead provide a function f_color() that takes as its only argument the number of colors to generate
flip	if TRUE (default), groups are rows and features are columns, and vice-verso for FALSE
do_plot	Whether to plot, logical
pt.size	size of jitter in the violin plots. Set to 0 (default) to omit
feature_fontface	"bold.italic"
fontsize_axistext_x	12, font size for x axis
fontsize_axistext_y	12, font size for y axis
aspect.ratio	NULL
figurenames	The filename and address of the output plot,
width	figure width
height	figure height

Value

ggplot2 object

Examples

load(system.file("extdata", "Pagwas_data.RData", package = "scPagwas"))
suppressMessages(library("ggsci"))
suppressMessages(library("Seurat"))
top5genes <- rownames(Pagwas_data@misc$gene_heritability_correlation)[order(
  Pagwas_data@misc$gene_heritability_correlation,
  decreasing = TRUE
)[1:5]]
plot_vln_Corgenes(
  seurat_obj = Pagwas_data,
  assay = "RNA", slot = "data",
  var_group = "anno",
  vec_features = top5genes,
  do_plot = TRUE
)

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