drugsens (version 0.1.0)

change_data_format_to_longer: Data format changer

Description

This function gets the count data data.frame, that has a wider format and it returns a longer-formatted data.frame

Usage

change_data_format_to_longer(
  .data,
  pattern_column_markers = "_ratio_of_total_cells",
  unique_name_row_identifier = "filter_image",
  additional_columns = TRUE
)

Value

A dataframe/tibble.

Arguments

.data

The markers count dataframe that is coming from the processing of the microscopy data

pattern_column_markers

The markers' pattern name to obtain the column with ratios of the markers (it defaults to "_ratio_of_total_cells")

unique_name_row_identifier

String that indicates the unique identifier for each image, defaults as "filter_image"

additional_columns

columns that can be additionally added to the longer formatted data.frame, "Defaults as c("Treatment", "PID", "Image_number", "Tissue", "Concentration", "DOC")"

Details

Reformat the counts data in longer format

Examples

# \donttest{
# Set up relabeling list
list_of_relabeling <- list(
  "PathCellObject" = "onlyDAPIPositve",
  "cCasp3" = "cCASP3",
  "E-Cadherin: cCASP3" = "E-Cadherin and cCASP3",
  "EpCAM_E-Cadherin" = "E-Cadherin",
  "EpCAM_E-Cadherin and cCASP3" = "E-Cadherin and cCASP3"
)

# Load and process example data
bind_data <- data_binding(
  path_to_the_projects_folder = system.file("extdata/to_merge/", package = "drugsens")
)
counts_dataframe <- make_count_dataframe(bind_data)

# Convert to long format
plotting_ready_dataframe <- change_data_format_to_longer(counts_dataframe)
# }