VisMultiModule {BioM2}

Visualisation of the results of the analysis of the pathway modules

Description

Visualisation of the results of the analysis of the pathway modules

Usage

VisMultiModule(
  BioM2_pathways_obj = NULL,
  FindParaModule_obj = NULL,
  ShowModule_obj = NULL,
  PathwaysModule_obj = NULL,
  exact = TRUE,
  ancestor_anno = NULL,
  type_text_table = FALSE,
  text_table_theme = ttheme("mOrange"),
  volin = FALSE,
  control_label = 0,
  module = NULL,
  cols = NULL,
  n_neighbors = 8,
  spread = 1,
  min_dist = 2,
  target_weight = 0.5,
  size = 1.5,
  alpha = 1,
  ellipse = TRUE,
  ellipse.alpha = 0.2,
  theme = ggthemes::theme_base(base_family = "serif"),
  save_pdf = FALSE,
  width = 7,
  height = 7
)

Arguments

BioM2_pathways_obj

Results produced by BioM2(,target='pathways')

FindParaModule_obj

Results produced by FindParaModule()

ShowModule_obj

Results produced by ShowModule()

PathwaysModule_obj

Results produced by PathwaysModule()

exact

Whether to divide GO pathways more accurately (work when ancestor_anno=NULL)

ancestor_anno

Annotations for ancestral relationships (like data('GO_Ancestor') )

type_text_table

Whether to display it in a table

text_table_theme

The topic of this table.Detail for ggtexttable()

volin

Can only be used when PathwaysModule_obj exists. ( Violin diagram )

control_label

Can only be used when PathwaysModule_obj exists. ( Control group label )

module

Can only be used when PathwaysModule_obj exists.( PathwaysModule ID )

cols

palette (vector of colour names)

n_neighbors

The size of local neighborhood (in terms of number of neighboring sample points) used for manifold approximation. Larger values result in more global views of the manifold, while smaller values result in more local data being preserved. In general values should be in the range 2 to 100.

spread

The effective scale of embedded points. In combination with min_dist, this determines how clustered/clumped the embedded points are.

min_dist

The effective minimum distance between embedded points. Smaller values will result in a more clustered/clumped embedding where nearby points on the manifold are drawn closer together, while larger values will result on a more even dispersal of points. The value should be set relative to the spread value, which determines the scale at which embedded points will be spread out.

target_weight

Weighting factor between data topology and target topology. A value of 0.0 weights entirely on data, a value of 1.0 weights entirely on target. The default of 0.5 balances the weighting equally between data and target. Only applies if y is non-NULL.

size

Scatter plot point size

alpha

Alpha for ellipse specifying the transparency level of fill color. Use alpha = 0 for no fill color.

ellipse

logical value. If TRUE, draws ellipses around points.

ellipse.alpha

Alpha for ellipse specifying the transparency level of fill color. Use alpha = 0 for no fill color.

theme

Default:theme_base(base_family = "serif")

save_pdf

Whether to save images in PDF format

width

image width

height

image height

Value

a ggplot2 object