R: Plot gene relevance or differential map

plot_differential_map {destiny}

R Documentation

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.

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'))