plot_mouse_tissue_devel: Nice plot to check expression and PSI across ENCODE mouse...

In Ni-Ar/niar: Nice Interactive Analysis with R

Nice plot to check expression and PSI across ENCODE mouse developmental stages of different tissues.

Description

Nice plot to check expression and PSI across ENCODE mouse developmental stages of different tissues.

Usage

plot_mouse_tissue_devel(
  data_tbl,
  title = NULL,
  legend = c("inside", "outside"),
  save_plot = FALSE,
  plot_name = NULL,
  out_plot_dir = NULL,
  width = 7,
  height = 7,
  colour_bar = c("BlueRed", "viridis"),
  PSI_limits = c(0, 100),
  blck_wht_PSI_col_thshld = 70
)

Arguments

data_tbl	A tibble generated with get_mouse_tissue_devel_tbl.
title	A title for the plot. By default (NULL) is "gene ~ vast-id".
legend	Either inside or outside for specifying the position of the legend relative to the plot.
save_plot	Logical, whether or not to save the plot as pdf.
plot_name	Name of the pdf plot file. By default (NULL) is a meaningful name.
out_plot_dir	Path specifying where to save the plot. By default (NULL) is dated subfolder.
width	Width of the plot in cm (numeric). Defaults are already very good.
height	Height of the plot in cm (numeric). Defaults are already very good.
colour_bar	Colour palette to represent the PSI values. Select between BlueRed or viridis.
PSI_limits	A vector of length 2, specifying the minimum and maximum PSI colour limits in the legend.
blck_wht_PSI_col_thshld	The PSI text is shown in black, PSI values above this threshold will be displayed in white instead. Gives better contrast with dark colours of high PSI.

Value

A ggplot2 plot or a pdf.

See Also

get_mouse_tissue_devel_tbl()

Examples

# Plot Pax6 expression and its exon 6 PSI 
get_mouse_tissue_devel_tbl(vst_id = "MmuEX0033804", ensembl_gene_id = "ENSMUSG00000027168")  |>
         plot_mouse_tissue_devel(legend = "inside", colour_bar = 'BlueRed')

Ni-Ar/niar documentation built on Feb. 3, 2025, 9:25 a.m.