FLAMES heetmap plots — plot_isoform

Plot expression heatmap of top n isoforms of a gene

Usage

plot_isoform_heatmap(
  sce,
  gene_id,
  transcript_ids,
  n = 4,
  isoform_legend_width = 7,
  col_low = "#313695",
  col_mid = "#FFFFBF",
  col_high = "#A50026",
  color_quantile = 1,
  cluster_palette,
  ...
)

Arguments

sce: The SingleCellExperiment object containing transcript counts, rowRanges and rowData with gene_id and transcript_id columns.
gene_id: The gene symbol of interest, ignored if transcript_ids is provided.
transcript_ids: The transcript ids to plot.
n: The number of top isoforms to plot from the gene. Ignored if transcript_ids is provided.
isoform_legend_width: The width of isoform legends in heatmaps, in cm.
col_low: Color for cells with low expression levels in UMAPs.
col_mid: Color for cells with intermediate expression levels in UMAPs.
col_high: Color for cells with high expression levels in UMAPs.
color_quantile: The lower and upper expression quantile to be displayed bewteen col_low and col_high, e.g. with color_quantile = 0.95, cells with expressions higher than 95% of other cells will all be shown in col_high, and cells with expression lower than 95% of other cells will all be shown in col_low.
cluster_palette: Optional, named vector of colors for the cluster annotations.
...: Additional arguments to pass to Heatmap.

Value

a ComplexHeatmap

Details

Takes SingleCellExperiment object and plots an expression heatmap with the isoform visualizations along genomic coordinates.

Examples

data(scmixology_lib10_transcripts)
scmixology_lib10_transcripts |>
  scuttle::logNormCounts() |>
  plot_isoform_heatmap(gene = "ENSG00000108107")
#> Constructing graphics...
#> Constructing graphics...
#> Constructing graphics...
#> Constructing graphics...