plotGeneLoadings: Generate t-SNE plots and gene loading plots

In rliger: Linked Inference of Genomic Experimental Relationships

Generate t-SNE plots and gene loading plots

Description

Plots t-SNE coordinates of all cells by their loadings on each factor. Underneath it displays the most highly loading shared and dataset-specific genes, along with the overall gene loadings for each dataset.

It is recommended to call this function into a PDF due to the large number of plots produced.

Usage

plotGeneLoadings(
  object,
  dataset1 = NULL,
  dataset2 = NULL,
  num.genes.show = 12,
  num.genes = 30,
  mark.top.genes = TRUE,
  factor.share.thresh = 10,
  log.fc.thresh = 1,
  umi.thresh = 30,
  frac.thresh = 0,
  pval.thresh = 0.05,
  do.spec.plot = TRUE,
  max.val = 0.1,
  pt.size = 0.4,
  option = "plasma",
  zero.color = "#F5F5F5",
  return.plots = FALSE,
  axis.labels = NULL,
  do.title = FALSE,
  verbose = TRUE,
  raster = NULL
)

Arguments

object	liger object. Should call runTSNE before calling.
dataset1	Name of first dataset (by default takes first two datasets for dataset1 and 2)
dataset2	Name of second dataset
num.genes.show	Number of genes displayed as y-axis labels in the gene loading plots at the bottom (default 12)
num.genes	Number of genes to show in word clouds (default 30).
mark.top.genes	Plot points corresponding to top loading genes in different color (default TRUE).
factor.share.thresh	Use only factors with a dataset specificity less than or equal to threshold (default 10).
log.fc.thresh	Lower log-fold change threshold for differential expression in markers (default 1).
umi.thresh	Lower UMI threshold for markers (default 30).
frac.thresh	Lower threshold for fraction of cells expressing marker (default 0).
pval.thresh	Upper p-value threshold for Wilcoxon rank test for gene expression (default 0.05).
do.spec.plot	Include dataset specificity plot in printout (default TRUE).
max.val	Value between 0 and 1 at which color gradient should saturate to max color. Set to NULL to revert to default gradient scaling. (default 0.1)
pt.size	Point size for plots (default 0.4).
option	Colormap option to use for ggplot2's scale_color_viridis (default 'plasma').
zero.color	Color to use for zero values (no expression) (default '#F5F5F5').
return.plots	Return ggplot objects instead of printing directly (default FALSE).
axis.labels	Vector of two strings to use as x and y labels respectively (default NULL).
do.title	Include top title with cluster and Dataset Specificity (default FALSE).
verbose	Print progress bar/messages (TRUE by default)
raster	Rasterization of points (default NULL). Automatically convert to raster format if there are over 100,000 cells to plot.

Value

List of ggplot plot objects (only if return.plots TRUE, otherwise prints plots to console).

Examples

ligerex <- createLiger(list(ctrl = ctrl, stim = stim))
ligerex <- normalize(ligerex)
ligerex <- selectGenes(ligerex)
ligerex <- scaleNotCenter(ligerex)
ligerex <- optimizeALS(ligerex, k = 5, max.iter = 1)
ligerex <- quantile_norm(ligerex)
ligerex <- runTSNE(ligerex)
plotGeneLoadings(ligerex, "stim", "ctrl", do.spec.plot = FALSE)

rliger documentation built on Nov. 9, 2023, 1:07 a.m.