plot_transcript_heatmap: Plot clustered heatmap

In pachterlab/sleuth: Tools for investigating RNA-Seq

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

pachterlab/sleuth documentation built on Nov. 17, 2022, 4:51 p.m.