Gene Relevance plotting {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

## 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, ...)

plot_differential_map(coords, exprs, ..., gene, dims = 1:2,
  pal = cube_helix, faceter = facet_wrap(~Gene))

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

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

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

plot_gene_relevance(coords, exprs, ..., iter_smooth = 2L, genes = 5L,
  dims = 1:2, pal = palette())

## S4 method for signature 'matrix,matrix'
plot_gene_relevance(coords, exprs, ...,
  iter_smooth = 2L, genes = 5L, dims = 1:2, pal = palette())

## S4 method for signature 'DiffusionMap,missing'
plot_gene_relevance(coords, exprs, ...,
  iter_smooth = 2L, genes = 5L, dims = 1:2, pal = palette())

## S4 method for signature 'GeneRelevance,missing'
plot_gene_relevance(coords, exprs, ...,
  iter_smooth = 2L, genes = 5L, dims = 1:2, pal = palette())

Arguments

x

GeneRelevance object.

y, gene

Gene name(s) or index/indices to create differential map for. (integer or character)

...

Passed to plot_differential_map/plot_gene_relevance.

coords

A DiffusionMap/GeneRelevance object or a cells \times dims matrix.

exprs

An cells \times genes matrix. Only provide if coords is a matrix.

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.

genes

Genes to based relevance map on or number of genes to use. (vector of strings or one number) You can also pass an index into the gene names. (vector of numbers or logicals with length > 1)

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, gene = c('Fgf4', 'Nanog'))


[Package destiny version 2.10.2 Index]