Bubble plot of features (KO/pathways/modules) per bin

Source: R/PLOT-plot_bubble.R

Generic bubble plot for RBIMS tables (KEGG/InterPro/Pfam/...). Supports "Abundance", "Binary", "Percentage", or "None" (precomputed). You can set axis labels via x_labs/y_labs directly (TRUE/FALSE/character). Extra ggplot2 layers can be passed via ... (theme(), guides(), etc.).

plot_bubble(
  tibble_ko,
  x_axis,
  y_axis,
  analysis = NULL,
  calc = NULL,
  data_experiment = NULL,
  color_character = NULL,
  order_bins = NULL,
  order_metabolism = NULL,
  color_pallet = NULL,
  range_size = NULL,
  x_labs = TRUE,
  y_labs = TRUE,
  text_x = NULL,
  text_y = NULL,
  ...
)

Arguments

tibble_ko

Tibble produced by mapping/get_subset/import functions.

x_axis

Bare column (usually Bin_name).

y_axis

Bare column (KO/pathway/module/etc.).

analysis

Optional string ("KEGG", "InterPro", etc.). Informative only.

calc

"Abundance", "Binary", "Percentage", or "None".

data_experiment

Optional metadata (joined by "Bin_name").

color_character

Bare column for color (metadata or tibble_ko).

order_bins

Optional character vector with desired bin order.

order_metabolism

Optional character vector with desired y order.

color_pallet

Optional character vector for manual color scale.

range_size

Numeric length-2 for point size range (default c(1,5)).

x_labs

TRUE uses x name, FALSE uses NULL, character sets label.

y_labs

TRUE uses y name, FALSE uses NULL, character sets label.

text_x

Numeric axis text size (default 7).

text_y

Numeric axis text size (default 7).

...

Extra ggplot2 layers (e.g., theme(...), guides(...)).