R: Plot clustered heatmap

plot_transcript_heatmap

R Documentation

Plot clustered heatmap

Description

Plot a clustered heatmap. The clustering is done by the hclust function.

Usage

plot_transcript_heatmap(obj, transcripts, units = "tpm", trans = "log",
  cluster_transcripts = FALSE, offset = 1, color_high = "#581845",
  color_mid = "#FFC300", color_low = "#DAF7A6", x_axis_angle = 50,
  annotation_cols = setdiff(colnames(obj$sample_to_covariates), "sample"),
  ...)

Arguments

`obj`	a `sleuth` object
`transcripts`	a vector of strings containing a list of transcripts to be plotted in a heatmap
`units`	a string specifying which units to use, either tpm or est_counts (scaled_reads_per_base for gene_mode)
`trans`	a function or a string specifying a function to transform the data by
`cluster_transcripts`	whether the transcripts also should be clustered. default is `FALSE`
`offset`	how much should be added to estimated expression before transformation? Default is 1.
`color_high`	the 'high expression' color (default: dark red)
`color_low`	the 'low expression' color (default: light green)
`x_axis_angle`	the angle at which to put the x-axis labels
`annotation_cols`	a character vector of covariates from `sample_to_covariates` that should be annotated on the heatmap
`...`	additional arguments to customize the heatmap. passed to `pheatmap`. See ?pheatmap for documentation on additional options.
`color_mide`	the 'medium expression' color (default: yellow)

Value

a ggplot object