plot_expression: Plot a heatmap given expression data
In ABAEnrichment: Gene expression enrichment in human brain regions

Description Usage Arguments Value Author(s) References See Also Examples

The function produces a (heatmap.2 from package gplots). To be used with gene-expression matrices obtained from get_expression.

1	plot_expression(expr_mat, dendro = TRUE, gene_vars = NULL, main = "")

`expr_mat`	matrix of expression values with genes in columns and brain regions in rows, like returned from `get_expression` (rownames are expected to be brain region identifiers, and their acronym is added automatically)
`dendro`	logical indicating whether rows and columns should be rearranged with a dendrogram based on row/column means (using `hclust`).
`gene_vars`	optional data.frame of gene-associated variables to be plotted as a colored sidebar. This can be the same input as for an enrichment analysis, i.e. a data.frame with genes in the first columns and with additional columns depending on the test used in `aba_enrich`. For a hypergeometric test the genes are grouped into candidate (red) and background genes (black); for the Wilcoxon rank-sum test, the side bar indicates the user-defined scores; for the binomial test the side bar shows A/(A+B) and for the 2x2 contingency table test ((A+1)/(B+1)) / ((C+1)/(D+1)) (+1 added to prevent division by 0).
`main`	optional character to use as a title for the heatmap.

Invisibly, a list with components

`rowInd`	row index permutation vector as returned by `order.dendrogram`
`colInd`	column index permutation vector.
`call`	the matched call
`carpet`	reordered 'x' values used to generate the main 'carpet'
`rowDendrogram`	row dendrogram, if present
`colDendrogram`	column dendrogram, if present
`breaks`	values used for color break points
`col`	colors used
`colorTable`	A three-column data frame providing the lower and upper bound and color for each bin

Steffi Grote

[1] Hawrylycz, M.J. et al. (2012) An anatomically comprehensive atlas of the adult human brain transcriptome, Nature 489: 391-399. doi: 10.1038/nature11405
[2] Miller, J.A. et al. (2014) Transcriptional landscape of the prenatal human brain, Nature 508: 199-206. doi: 10.1038/nature13185
[3] Allen Institute for Brain Science. Allen Human Brain Atlas. Available from: http://human.brain-map.org/
[4] Allen Institute for Brain Science. BrainSpan Atlas of the Developing Human Brain. Available from: http://brainspan.org/

browseVignettes("ABAEnrichment")
browseVignettes("ABAData")
get_expression
aba_enrich
get_name
get_id
get_sampled_substructures
get_annotated_genes
heatmap.2
hclust

## plot expression data of six genes in two brain regions
## from children (age_category 3)
expr = get_expression(structure_ids=c("Allen:10657","Allen:10208"),
    gene_ids=c('RFFL', 'NTS', 'LIPE', 'GALNT6', 'GSN', 'BTBD16', 'CERS2'),
    dataset="5_stages")
expr_age_3 = expr[[3]]
plot_expression(expr_age_3)

## see the package vignette for more examples