DotPlotCompare: DotPlotCompare
In KidneyRegeneration/DevKidCC: Developing Kidney Cell Classifier

View source: R/visualisation.R

DotPlotCompare

R Documentation

DotPlotCompare

Description

DotPlotCompare

Usage

DotPlotCompare(
  new.object = NULL,
  show = "gene",
  split.by = "orig.ident",
  scaling = "log",
  size = "pct.exp",
  idents = "all",
  classification = "DKCC",
  dot.min = 0.1,
  dot.scale = 6,
  col.min = NA,
  col.max = NA,
  scale.min = NA,
  scale.max = NA,
  scale.by = "radius",
  features,
  compare.to.organoids = FALSE,
  filter.samples = NULL,
  columns = NULL
)

Arguments

`new.object`	seurat object to compare to reference data
`show`	this defines the focus of the output; "gene" partitions by gene, anything else partitions by segment
`split.by`	meta.data column to split the sample by, usually the sample column
`scaling`	choose "log", "scale" or "raw" to change how the expression values are displayed
`size`	how to scale the size of the dot, "pct.exp" for the percent of cells expressing the gene, "Pct" is percent of cells in identity
`idents`	Identities to display. Use "all" to show all segments, "nephron" to show all nephron segments, "others" to show all non-nephron segments, or a string of identities to select specific Identities
`classification`	choose "DKCC" or "LineageID"
`dot.min`	dot size of minimum cell percentage
`dot.scale`	dot size of maximum cell percentage
`col.min`	minimum expression value to plot
`col.max`	maximum expression value to plot
`scale.min`	minimum scale
`scale.max`	maximum scale
`scale.by`	"radius" or "size"
`features`	features to plot
`compare.to.organoids`	if function should plot organoid samples from the database
`filter.samples`	if compare.to.organoids=T, can provide desired sample names here using the output from "GetSampleIDs".
`columns`	how many columns to plot. Default is to plot as square as possible.