plot_expression: Plot a heatmap given expression data

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

View source: R/plot_expression.R

Description

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

Usage

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

Arguments

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.

Value

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

Author(s)

Steffi Grote

References

[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/

See Also

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

Examples

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## 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

ABAEnrichment documentation built on Nov. 1, 2018, 2:09 a.m.