Process data as the shiny application — process

A utility function for reading a processing the data as `tagtango' does.

Usage

process_data(
  filename,
  data_type,
  left,
  right,
  pc1_axis1 = NULL,
  pc1_axis2 = NULL,
  pc2_axis1 = NULL,
  pc2_axis2 = NULL,
  filter_variable = NULL,
  filter_values = NULL,
  grouping_variable = NULL,
  grouping_values = NULL,
  min_counts = NULL,
  dimension = NULL,
  input_data = NULL
)

Arguments

filename: path to data file
data_type: experiment used in the MultiAssayExperiment or data contained in logcounts in SingleCellExperiment
left: annotation in the left of the diagram
right: annotation in the right of the diagram
pc1_axis1: first axis of first dimension reduction space
pc1_axis2: second axis of first dimension reduction space
pc2_axis1: first axis of second dimension reduction space
pc2_axis2: second axis of second dimension reduction space
filter_variable: filtering variable found in `dat'
filter_values: values in `filter_variable' that need to be excluded
grouping_variable: grouping variable found in `dat'
grouping_values: values in `grouping_variable' that need to be filtered
min_counts: minimum number of cells in a link for this to be displayed
dimension: internal variable to determine whether the data is a data frame (=0), a low-dimension dataset (=1), or a high-dimension dataset (=2).
input_data: object inputed directly.

Value

Returns a list containing two attributes: data and network. The first contains the data filtered according to the grouping and filtering values. The second, contains the data organized in a manner that is readible by the sankeyNetwork.