Plot a clustered heatmap. The clustering is done by the hclust function.
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"),
...)a sleuth object
a vector of strings containing a list of transcripts to be plotted in a heatmap
a string specifying which units to use, either tpm or est_counts (scaled_reads_per_base for gene_mode)
a function or a string specifying a function to transform the data by
whether the transcripts also should be clustered.
default is FALSE
how much should be added to estimated expression before transformation? Default is 1.
the 'high expression' color (default: dark red)
the 'low expression' color (default: light green)
the angle at which to put the x-axis labels
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.
the 'medium expression' color (default: yellow)
a ggplot object