Plot the gene patters for given ids.
plotGeneClusterPatterns(
genesList,
ids,
additionalID,
max_gap = 1e+07,
colors,
maxNonEssential = 5,
alignType = c("local", "global"),
label_size = 0.5
)Arguments
- genesList
A list of GRanges.
- ids
IDs to be plotted. See getGeneCluster.
- additionalID
Other IDs should be included.
- max_gap
The maximal gaps from the first ID in `ids`.
- colors
The colors for genes
- maxNonEssential
The maximal number for non-essential genes between two essential genes.
- alignType
Align the gene pattern by query gene ('local') or by the clusters ('global').
- label_size
The label cex value. default is 0.5.
Value
invisible list of plot data.
Examples
fish <- readRDS(system.file('extdata', 'fish.rds',
package = 'geneClusterPattern'))
homologs <- readRDS(system.file('extdata', 'homologs.rds',
package = 'geneClusterPattern'))
queryGene <- 'inhbaa'
nearestNeighbors <- getGeneCluster(fish, queryGene, homologs)
genesList <- c(drerio=fish, homologs)
pgp <- plotGeneClusterPatterns(genesList, nearestNeighbors)
