Gene-Relevance-plotting: Plot gene relevance or differential map

In theislab/destiny: Creates diffusion maps

Plot gene relevance or differential map

Description

plot(gene_relevance, 'Gene') plots the differential map of this/these gene(s), plot(gene_relevance) a relevance map of a selection of genes. Alternatively, you can use plot_differential_map or plot_gene_relevance on a GeneRelevance or DiffusionMap object, or with two matrices.

Usage

plot_differential_map(
  coords,
  exprs,
  ...,
  genes,
  dims = 1:2,
  pal = hcl.colors,
  faceter = facet_wrap(~Gene)
)

## S4 method for signature 'matrix,matrix'
plot_differential_map(
  coords,
  exprs,
  ...,
  genes,
  dims = 1:2,
  pal = hcl.colors,
  faceter = facet_wrap(~Gene)
)

## S4 method for signature 'DiffusionMap,missing'
plot_differential_map(
  coords,
  exprs,
  ...,
  genes,
  dims = 1:2,
  pal = hcl.colors,
  faceter = facet_wrap(~Gene)
)

## S4 method for signature 'GeneRelevance,missing'
plot_differential_map(
  coords,
  exprs,
  ...,
  genes,
  dims = 1:2,
  pal = hcl.colors,
  faceter = facet_wrap(~Gene)
)

plot_gene_relevance(
  coords,
  exprs,
  ...,
  iter_smooth = 2L,
  n_top = 10L,
  genes = NULL,
  dims = 1:2,
  pal = palette(),
  col_na = "grey",
  limit = TRUE
)

## S4 method for signature 'matrix,matrix'
plot_gene_relevance(
  coords,
  exprs,
  ...,
  iter_smooth = 2L,
  n_top = 10L,
  genes = NULL,
  dims = 1:2,
  pal = palette(),
  col_na = "grey",
  limit = TRUE
)

## S4 method for signature 'DiffusionMap,missing'
plot_gene_relevance(
  coords,
  exprs,
  ...,
  iter_smooth = 2L,
  n_top = 10L,
  genes = NULL,
  dims = 1:2,
  pal = palette(),
  col_na = "grey",
  limit = TRUE
)

## S4 method for signature 'GeneRelevance,missing'
plot_gene_relevance(
  coords,
  exprs,
  ...,
  iter_smooth = 2L,
  n_top = 10L,
  genes = NULL,
  dims = 1:2,
  pal = palette(),
  col_na = "grey",
  limit = TRUE
)

plot_gene_relevance_rank(
  coords,
  exprs,
  ...,
  genes,
  dims = 1:2,
  n_top = 10L,
  pal = c("#3B99B1", "#F5191C"),
  bins = 10L,
  faceter = facet_wrap(~Gene)
)

## S4 method for signature 'matrix,matrix'
plot_gene_relevance_rank(
  coords,
  exprs,
  ...,
  genes,
  dims = 1:2,
  n_top = 10L,
  pal = c("#3B99B1", "#F5191C"),
  bins = 10L,
  faceter = facet_wrap(~Gene)
)

## S4 method for signature 'DiffusionMap,missing'
plot_gene_relevance_rank(
  coords,
  exprs,
  ...,
  genes,
  dims = 1:2,
  n_top = 10L,
  pal = c("#3B99B1", "#F5191C"),
  bins = 10L,
  faceter = facet_wrap(~Gene)
)

## S4 method for signature 'GeneRelevance,missing'
plot_gene_relevance_rank(
  coords,
  exprs,
  ...,
  genes,
  dims = 1:2,
  n_top = 10L,
  pal = c("#3B99B1", "#F5191C"),
  bins = 10L,
  faceter = facet_wrap(~Gene)
)

## S4 method for signature 'GeneRelevance,character'
plot(x, y, ...)

## S4 method for signature 'GeneRelevance,numeric'
plot(x, y, ...)

## S4 method for signature 'GeneRelevance,missing'
plot(x, y, ...)

Arguments

coords	A DiffusionMap/GeneRelevance object or a cells \times dims matrix.
exprs	An cells \times genes matrix. Only provide if coords is a matrix.
...	Passed to plot_differential_map/plot_gene_relevance.
genes	Genes to base relevance map on (vector of strings). You can also pass an index into the gene names (vector of numbers or logicals with length > 1). The default NULL means all genes.
dims	Names or indices of dimensions to plot. When not plotting a GeneRelevance object, the relevance for the dimensions 1:max(dims) will be calculated.
pal	Palette. Either A colormap function or a list of colors.
faceter	A ggplot faceter like facet_wrap(~ Gene).
iter_smooth	Number of label smoothing iterations to perform on relevance map. The higher the more homogenous and the less local structure.
n_top	Number the top n genes per cell count towards the score defining which genes to return and plot in the relevance map.
col_na	Color for cells that end up with no most relevant gene.
limit	Limit the amount of displayed gene labels to the amount of available colors in pal?
bins	Number of hexagonal bins for plot_gene_relevance_rank.
x	GeneRelevance object.
y	Gene name(s) or index/indices to create differential map for. (integer or character)

Value

ggplot2 plot, when plotting a relevance map with a list member $ids containing the gene IDs used.

See Also

gene_relevance, Gene Relevance methods

Examples

data(guo_norm)
dm <- DiffusionMap(guo_norm)
gr <- gene_relevance(dm)
plot(gr)          # or plot_gene_relevance(dm)
plot(gr, 'Fgf4')  # or plot_differential_map(dm, 'Fgf4')

guo_norm_mat <- t(Biobase::exprs(guo_norm))
pca <- prcomp(guo_norm_mat)$x
plot_gene_relevance(pca, guo_norm_mat, dims = 2:3)
plot_differential_map(pca, guo_norm_mat, genes = c('Fgf4', 'Nanog'))

theislab/destiny documentation built on Jan. 27, 2024, 9:57 p.m.