Single feature plot function

Creates a single plot or faceted plot for a given feature or gene across the selected tissues. Single plots are optimized for H = 1.54 in and W = 1.225 inches. If a right hand legend is added, the width should be 1.715. This can be toggled as needed by saving output and editing as a ggplot object

Usage

plot_single_feature(
  feature,
  selected_tissues = "all",
  selected_omes = "all",
  p_level = 0.05,
  output_file = NULL,
  scale_factor = 1,
  color_time_labels = FALSE,
  include_legend = TRUE,
  legend_position = "right",
  verbose = TRUE,
  epigen = FALSE
)

Arguments

feature

A single character string corresponding to a feature_id, gene_symbol, or refmet_name within the human feature-to-gene table

selected_tissues

character; one of tissue_available_list.

selected_omes

character; one of ome_available_list.

p_level

Numeric threshold for adjusted p value significance in differential analysis (so this would make individual points highlighted in black if below this threshold)

output_file

a file path if desired, to autoatically save output in the standard size of height 1.54, width 1.225, recommended if output is known to be a single plot, not faceted

scale_factor

simple way to scale plot if larger sizes are needed for posters or talks. recommend integers only

color_time_labels

toggle TRUE/FALSE allows color tiles corresponding to time point colors to be used instead of x-axis

include_legend

toggle TRUE/FALSE to include a legend

legend_position

if include_legend == TRUE, position can be selected

verbose

logical; toggle to include verbose information

epigen

logical; toggle to include epigenetic features (only atac offered for this function). If you include a gene name, this could result in many many epigenetic features mapping to the one object.

Value

a ggplot

Author

Daniel Katz and Christopher Jin

Examples

if (FALSE) { # \dontrun{
plot_single_feature_test(feature="CAR 10:0",
  p_level = 0.05,
  selected_tissues = "all",
  selected_omes = "all",
  output_file = paste0("~/single_plot_test_scale.pdf"),
  scale_factor = 1,
  color_time_labels = F) +
theme(legend.position = "bottom")


plot_single_feature_test(feature="TFEB",
 p_level = 0.05,
 selected_tissues = "muscle",
 selected_omes = "prot-pr",
 output_file = paste0("~/single_plot_test_scale_tfeb_prot.png"),
 scale_factor = 1,
 color_time_labels = T,
 include_legend = F)
 } # }