rliger (version 1.0.0)

plotGeneLoadings: 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 = 0.1,
  option = "plasma",
  zero.color = "#F5F5F5",
  return.plots = FALSE,
  axis.labels = NULL,
  do.title = FALSE,
  verbose = TRUE
)

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 0.1).

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)

Value

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

Examples

# NOT RUN {
# ligerex (liger object based on in-memory datasets), factorization complete
ligerex <- quantile_norm(ligerex)
ligerex <- runUMAP(ligerex)
# pdf("gene_loadings.pdf")
plotGeneLoadings(ligerex, num.genes = 20)
# dev.off()
# ligerex (liger object based on datasets in HDF5 format), factorization complete input
ligerex <- readSubset(ligerex, slot.use = "norm.data", max.cells = 5000)
plotGeneLoadings(ligerex, num.genes = 20)
# }
# NOT RUN {
# }