Lineage Plot: Heatmap of Queries vs Lineages — plotLineageQuery • MolEvolvR

Lineage plot for queries. Heatmap.

Usage

plotLineageQuery(
  query_data = all,
  queries,
  colname = "ClustName",
  cutoff,
  color = "default"
)

Arguments

query_data: Data frame of protein homologs with the usual 11 columns + additional word columns (0/1 format). Default is prot (variable w/ protein data).
queries: Character Vector containing the queries that will be used for the categories.
colname: Character. The column used for filtering based on the queries. Default is "ClustName".
cutoff: Numeric. The cutoff value for filtering rows based on their total count. Rows with values below this cutoff are excluded.
color: Character. Defines the color palette used for the heatmap. Default is a red gradient.

Value

A ggplot object representing a heatmap (tile plot) showing the relationship between queries and lineages, with the intensity of color representing the count of matching records.

Note

Please refer to the source code if you have alternate file formats and/or column names.

Author

Janani Ravi, Samuel Chen

Examples

if (FALSE) { # \dontrun{
plotLineageQuery(prot, c("PspA", "PspB", "PspC", "PspM", "PspN"), 95)
} # }