Visualise and compare the performances of integration algorithms

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 = c("rank", "score", "none"),
  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 some scores or integrations are excluded. 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. One of 'rank' (default), 'score' or 'none'. The first two enable rescaling on ranks and scores respectively, while 'none' disables rescaling. Rescaling ensures that each metric equally contributes to the overall scores. 'rank' is more stable to changes in integrations included. Has no effect when recompute.overall.scores = FALSE.
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

Details

The rescale parameter controls how scores are rescaled prior to computing overall scores. Thus, when rescale != 'none', recompute.overall.scores should be TRUE (default). Otherwise, the overall scores will no longer match the scores displayed on the plot.

Albeit the min-max rescaling of scores in Luecken M.D. et al., 2022 is achievable with rescale = 'score', min-max rescaling on ranks (rescale = 'rank') is the default. Indeed, it results in more stable rankings of overall scores when the list of integrations to plot is modified.

To plot non-rescaled scores, make sure to use ScaleScores(..., rescale = "none") beforehand. To plot rescaled scores however, the rescale parameter of ScaleScores has no impact on the scores obtained for plotting.

References