rliger: plotGeneLoadings – R documentation

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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)

## End(Not run)

rliger

Linked Inference of Genomic Experimental Relationships

v1.0.0

GPL-3

Authors

Joshua Welch [aut, ctb], Chao Gao [aut, ctb, cre], Jialin Liu [aut, ctb], Joshua Sodicoff [aut, ctb], Velina Kozareva [aut, ctb], Evan Macosko [aut, ctb], Paul Hoffman [ctb], Ilya Korsunsky [ctb], Robert Lee [ctb]

Initial release

2021-04-18