Visualize as barplot

Visualize genes and it's transcript proportions in a barplot.

plot_proportion_barplot(
  dturtle,
  genes = NULL,
  meta_gene_id = NULL,
  group_colors = NULL,
  fit_line_color = "red",
  text_size = 11,
  label_angle = c(25, 1, 1),
  savepath = NULL,
  filename_ext = "_barplot.png",
  add_to_table = FALSE,
  BPPARAM = BiocParallel::SerialParam(),
  ...
)

Arguments

dturtle	dturtle result object of posthoc_and_stager().
genes	Character vector of genes to plot. If NULL, defaults to all found significant genes (sig_genes).
meta_gene_id	Optionally specify the column name in meta_table_gene, which contains real gene identifiers or gene names.
group_colors	Optionally specify the colours for the two sample groups in the plot. Must be a named vector, with the group names as names.
fit_line_color	Optionally specify the colour to use for the mean fit line.
text_size	Specify basic text size (in pt) to use in plot.
label_angle	Specify the angle of the x-axis labels, the vjust and hjust value (in that order).
savepath	If you want your files to be saved to disk, specify a save path here. The directories will be created if necessary.
filename_ext	Optionally specify a file name extension here, which also defines the save image format. The file name will be 'gene_name+extension'.
add_to_table	If a savepath is provided, add the filepaths of the created plots to the corresponding entries in dtu_table. The name of the column that shall be created can be specified here.
BPPARAM	If multicore processing should be used, specify a BiocParallelParam object here. Among others, can be SerialParam() (default) for non-multicore processing or MulticoreParam('number_cores') for multicore processing. See BiocParallel for more information.
...	Arguments passed on to ggplot2::ggsave filename File name to create on disk. plot Plot to save, defaults to last plot displayed. device Device to use. Can either be a device function (e.g. png()), or one of "eps", "ps", "tex" (pictex), "pdf", "jpeg", "tiff", "png", "bmp", "svg" or "wmf" (windows only). path Path of the directory to save plot to: path and filename are combined to create the fully qualified file name. Defaults to the working directory. scale Multiplicative scaling factor. width Plot size in units ("in", "cm", or "mm"). If not supplied, uses the size of current graphics device. height Plot size in units ("in", "cm", or "mm"). If not supplied, uses the size of current graphics device. units Plot size in units ("in", "cm", or "mm"). If not supplied, uses the size of current graphics device. dpi Plot resolution. Also accepts a string input: "retina" (320), "print" (300), or "screen" (72). Applies only to raster output types. limitsize When TRUE (the default), ggsave will not save images larger than 50x50 inches, to prevent the common error of specifying dimensions in pixels.

Value

Returns list of saved plots, for adding to the DTU table. If no savepath is provided, returns a list of the created plots for further processing. If add_to_table is provided, return the altered dturtle object, if at least one of the plots could be added to the DTU summary table.

Details

Shows the transcripts proportional change per analysis group, together with the mean fit value via a horizontal line. Significant transcript's names are marked in red.

See also

run_drimseq() and posthoc_and_stager() for DTU object creation. create_dtu_table() and plot_dtu_table() for table visualization.

Other DTUrtle visualization: create_dtu_table(), plot_dimensional_reduction(), plot_proportion_pheatmap(), plot_transcripts_view()