plotAssignmentScores: Plot Assignment Scores

In khodosevichlab/CellAnnotatoR: Automated marker-based cell type annotation

Plot Assignment Scores

Description

plot assignment scores on a separate scatterplot for each cell type

Usage

plotAssignmentScores(
  embedding,
  scores,
  classification.tree,
  parent.node = "root",
  build.panel = T,
  n.col = NULL,
  n.row = NULL,
  title.size = 12,
  ...
)

Arguments

scores	assignment scores. Can be obtained with 'assignCellsByScores'
classification.tree	cell type hierarchy represented by graph. Part of 'clf_data' object from 'getClassificationData'
parent.node	cell type, which subtypes' scores must be plotted
build.panel	combine individual plots to a single panel
n.col	number of columns in the panel
n.row	number of rows in the panel
title.size	font size for title of individual plots. Used only if build.panel==T
...	Arguments passed on to conos::embeddingPlot

Value

panel of plots if 'build.panel==T' or 'plot.list' otherwise

Examples

  clf_data <- getClassificationData(cm, marker_path)
  ann_by_level <- assignCellsByScores(graph, clf_data)
  plotAssignmentScores(t_sne, ann_by_level$scores$l1, clf_data$classification.tree)

khodosevichlab/CellAnnotatoR documentation built on June 29, 2022, 9:12 p.m.