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Visualise and compare the performances of integration algorithms

Source: R/scores.R
PlotScores.Rd

Plot the scaled integration scores to compare the obtained integrations

Usage

PlotScores(
  object,
  plot.type = c("dot", "radar", "lollipop"),
  split.by.score.type = TRUE,
  order.by = c("score", "name", "asis"),
  hide.zeros = FALSE,
  include.integration = NULL,
  exclude.integration = NULL,
  include.score = NULL,
  exclude.score = NULL,
  recompute.overall.scores = TRUE,
  rescale = TRUE,
  batch.coeff = 0.4,
  bio.coeff = 0.6,
  point.max.size = 20L,
  use.ggforce = is_installed("ggforce")
)

Arguments

object

a Seurat object

plot.type

one of 'table' (default), 'radar' or 'lollipop'. Type of desired plot

split.by.score.type

whether to split scores by type (bio-conservation, batch correction and overall scores). When set to FALSE, all scores are mixed in a single figure.

order.by

one of 'score' (default), 'name' or 'asis'. Determines the order of integrations in the legend (and on the y-axis for lolliplop and table plots). Scores are ordered by decreasing overall score by default, by name or by row-order when setting 'name' and 'asis' respectively.

hide.zeros

whether zero(ed) scores should be visible on the plot.

include.integration

name of the integration(s) to include. The default value (NULL) enable to include them all.

exclude.integration

name of the integration(s) to exclude. The default value (NULL) enable to include them all.

include.score

name of the score(s) to include. The default value (NULL) enable to include them all.

exclude.score

name of the score(s) to exclude. The default value (NULL) enable to include them all.

recompute.overall.scores

whether to recompute overall scores. Useful when there is a restriction on scores to plot. When FALSE, coefficient parameters have no impact.

rescale

whether to rescale each score between 0 and 1 using min-max normalisation before computing overall scores. This ensures that each metric equally contributes to the overall scores. Has no effect when recompute.overall.scores = FALSE. TRUE by default

batch.coeff

the weight of batch correction performance evaluation scores in the overall score.

bio.coeff

the weight of bio-conservation performance evaluation scores in the overall score.

point.max.size

inoperative unless plot.type = 'table' and use.ggforce = FALSE. Determine the maximum size of the points (only achieved for a score of 1) to fit the plotting area (handled automaticaly when ggforce is used).

use.ggforce

for plot.type = 'table', enable or disable the use of ggforce to draw the circles. Used by default when the package is installed

Value

a ggplot object