plot_bubble_for_genes_per_cluster: Plot bubble-plot for gene expression per cluster

In supatt-lab/SingCellaR: SingCellaR: an integrative analysis tool for single-cell RNA sequencing (scRNA-seq) data

Plot bubble-plot for gene expression per cluster

Description

Plot bubble-plot for gene expression per cluster

Usage

plot_bubble_for_genes_per_cluster(
  object,
  cluster.type = c("louvain", "kmeans"),
  gene_list = c(),
  point.color1 = "orange",
  point.color2 = "firebrick",
  buble.scale = 6,
  gene.font.size = 12,
  axist.x.font.size = 12,
  show.percent = FALSE,
  log = T,
  font.size.in.bubble = 2,
  IsApplyClustering = TRUE,
  IsClusterByRow = TRUE,
  clustering_method = "complete",
  IsClusterByColumn = TRUE,
  IsCustomOrder = FALSE,
  IsCustomOrderByRow = FALSE,
  IsCustomOrderByColumn = FALSE,
  row.custom.order = "",
  column.custom.order = ""
)

Arguments

object	The SingCellaR object.
cluster.type	The clustering method name.
gene_list	The vector of gene names.
point.color1	The color for low expression level. Default orange
point.color2	The color for high expression level. Default firebrick
buble.scale	The scale size of the bubble. Default 6
gene.font.size	The font size of gene name. Default 12
axist.x.font.size	The label on the x-axis font size. Default 12
show.percent	is logical. If TRUE, the percentage will be displayed.
log	is logical. If TRUE, the log expression will be applied.
font.size.in.bubble	The font size inside the bubble. Default 2
IsApplyClustering	is logical. If TRUE, the bubble plot will be clustered by using HCL.
IsClusterByRow	is logical. If TRUE, clustering by row.
clustering_method	The clustering method. Default 'complete'
IsClusterByColumn	is logical. If TRUE, clustering by column.
IsCustomOrder	is logical, If TRUE, the input custom order of row and column will be used.
IsCustomOrderByRow	is logical, If TRUE, row will be ordered by the custom input.
IsCustomOrderByColumn	is logical, If TRUE, column will be ordered by the custom input.
row.custom.order	is the vector of custom row names.
column.custom.order	is the vector of custom column names.

supatt-lab/SingCellaR documentation built on Aug. 24, 2023, 5:49 p.m.