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Waterfall component of WFPHM

wfphm_wf.Rd

Waterfall component of WFPHM

Usage

wfphm_wf_UI(id)

wfphm_wf_server(
  id,
  bm_dataset,
  group_dataset,
  cat_var,
  par_var,
  visit_var,
  subjid_var,
  value_vars,
  .default_group_palette = function(x) {
     pal_get_cat_palette(x,
    viridisLite::viridis(length(unique(x))))
 },
  bar_group_palette = list(),
  margin
)

Arguments

id

Shiny ID [character(1)]

cat_var, par_var, visit_var, subjid_var

[character(1)]

columns used as indicated in the details section

value_vars

[character(1+)]

possible colum values. If column is labelled, label will be displayed in the value menu

bar_group_palette

[list(palettes)]

list of custom palettes to apply to bar_grouping. It receives the values used for grouping and must return a DaVinci palette. Each palette is applied when the name of the entry in the list matches the name of the column used for grouping

margin

[numeric(4) | shiny::reactive(numeric(4)) | shinymeta::metaReactive(numeric(4))]

margin to be used on each of the sides. It must contain four entries named top, bottom, left and right

dataset

[shiny::reactive(data.frame) | shinymeta::metaReactive(data.frame)]

It expects the following format:

  • it contains, at least, the columns specified in the parameters: cat_var, par_var, value_vars, visit_var and subjid_var

  • cat_var, par_var, visit_var and subjid_var columns are factors

Value

UI

A bar plot

Server

A list with two entries:

  • margin: similar to the margin parameter with the minimum margins for the current plot

  • sorted_x: From the subsetted data the x levels sorted from high to low by y

Details

Data subsetting:

  • Allows selecting a column from all factor or character columns, from now on grouping_selection.

    • Menu labelled: Grouping

  • Data selection for plotting can be done in two modes switched by:

    • Menu labelled: Display demographic baseline information

Mode 1:

  • Allows selecting a column from the set of all numerical columns, from now on value_selection.

    • Menu labelled: Value

  • Subsets the dataset to the columns grouping_selection, subj_var and value_selection.

  • Removes all repeated rows from the dataset

  • If more than one row have the same subj_var an informative error indicating the plot cannot be created is shown.

Mode 2:

  • Allows selecting a value from the cat_var column, from now on cat_selection and a value from the par_var column from the subset of rows where par_cat is equal to cat_selection from now on par_selection.

    • Menu labelled: Category and Parameter

  • Allows selecting between the columns defined in val_var from now on value_selection.

    • Menu labelled: Value

  • Allows selecting a value from visit_var column, from now on visit_selection.

    • Menu labelled: Visit

  • Subsets the dataset rows where:

    • visit_var equal to visit_selection

    • par_var equal to par_selection

  • Subsets the dataset to the grouping_selection, the subj_var and the value_selection.

  • If more than one row have the same subj_var an informative error indicating the plot cannot be created is shown.

Then the dataset is prepared to be passed to bar_D3:

  • subj_var becomes x column

  • val_selection becomes y column

  • the label attribute of y column is either value_selection in Mode 1 or par_selection in Mode 2

  • grouping_selection becomes z column

  • grouping_selection becomes label column

Completing the dataset:

  • Subset dataset will be completed in the following way. If any level in x is not present in the subset dataset, but it was present in the subj_var column in the original dataset, a row is added where x is equal to the missing value y is NA and z is NA.

Data outliers:

  • Allows setting two limits upper and lower, values above or below in the subsetted dataset will be considered outliers. Rows considered outliers will have the column:

    • label replaced by "outlier"

    • color equal to "gray"

  • Rows not considered outliers will have the column:

    • color equal to NA

X axis sorting

  • x levels are sorted from greater to lower value in y

Then a call to bar_D3 is done with the following arguments:

  • data = subset dataset (as described above)

  • x_axis = NULL

  • y_axis = W

  • z_axis = NULL

  • margin is the parameter passed to this same function

  • palette is hardcoded with 8 colors. After 8 categories colors are repeated

  • msg_func = NULL

  • quiet = TRUE

Functions

  • wfphm_wf_UI(): UI

  • wfphm_wf_server(): server