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Make an interactive faceted boxplot of the top differential genes in a contrast

Source: R/topgeneboxplot.R
interactive_topgene_boxplots.Rd

The plotly equivalent of static_topgene_boxplots. One subplot is drawn per gene, with samples grouped by condition. The beeswarm overlay is approximated using plotly's native jittered box points, since all of the (typically few) per-sample values are drawn and shipping ggbeeswarm's point layout to the browser isn't necessary here.

Usage

interactive_topgene_boxplots(
  assay,
  groupby,
  genes,
  annotations = NULL,
  labels = NULL,
  beeswarm = TRUE,
  ncol = NULL,
  palette = NULL,
  palette_name = COLORBLIND_PALETTE_NAME,
  expressiontype = "expression",
  should_transform = NULL
)

Arguments

assay

Numeric matrix, genes (rows) by samples (columns)

groupby

Vector of group labels, one per column of assay

genes

Character vector of row names of assay to facet on, in the order facets should appear. Also used to look up values in assay, so must match its row names even when labels is supplied.

annotations

Optional named character vector keyed by the values in genes, rendered as a per-facet annotation (e.g. a q value string)

labels

Optional named character vector keyed by the values in genes, used as the facet title in place of the raw gene identifier (e.g. a gene symbol where genes holds Ensembl IDs). Genes missing from labels fall back to their raw identifier. genes itself still drives the lookup into assay and the matching of annotations.

beeswarm

Overlay individual points using geom_quasirandom?

ncol

Number of facet columns. Defaults to min(3, length(genes))

palette

Palette of colours, one for each unique value of groupby

palette_name

Valid R color palette name

expressiontype

Expression type for use in y axis label

should_transform

A boolean indicating if the log2 transformation should be applied. If TRUE, log2 transformation is applied unconditionally. If FALSE, no transformation is applied. If NULL, a conditional transformation based on threshold is applied.

Value

output A plotly output

Examples

require(airway)
data(airway, package = "airway")
mat <- assays(airway)[[1]][1:4, ]
groupby <- as.character(colData(airway)$dex)
interactive_topgene_boxplots(mat, groupby, rownames(mat))