stitchFieldCoordinates#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/general_help.R#L184

Description#

Helper function to stitch field coordinates together to form one complete picture

Usage#

stitchFieldCoordinates(
  location_file,
  offset_file,
  cumulate_offset_x = F,
  cumulate_offset_y = F,
  field_col = "Field of View",
  X_coord_col = "X",
  Y_coord_col = "Y",
  reverse_final_x = F,
  reverse_final_y = T
)

Arguments#

Argument

Description

location_file

location dataframe with X and Y coordinates

offset_file

dataframe that describes the offset for each field (see details)

cumulate_offset_x

(boolean) Do the x-axis offset values need to be cumulated?

cumulate_offset_y

(boolean) Do the y-axis offset values need to be cumulated?

field_col

column that indicates the field within the location_file

X_coord_col

column that indicates the x coordinates

Y_coord_col

column that indicates the x coordinates

reverse_final_x

(boolean) Do the final x coordinates need to be reversed?

reverse_final_y

(boolean) Do the final y coordinates need to be reversed?

Details#

Stitching of fields:

  • list(“1. have cell locations:?) list(“at least 3 columns: field, X, Y?)

  • list(“2. create offset file:?) list(“offset file has 3 columns: field, x_offset, y_offset?)

  • list(“3. create new cell location file by stitching original cell locations with stitchFieldCoordinates?)

  • list(“4. provide new cell location file to?, list(list(“createGiottoObject?)))

Value#

Updated location dataframe with new X [‘X_final’] and Y [‘Y_final’] coordinates