stitchFieldCoordinates: stitchFieldCoordinates

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

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

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:

• 1. have cell locations: at least 3 columns: field, X, Y

• 2. create offset file: offset file has 3 columns: field, x_offset, y_offset

• 3. create new cell location file by stitching original cell locations with stitchFieldCoordinates

• 4. provide new cell location file to createGiottoObject

Value

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

bernard2012/Giotto documentation built on Sept. 22, 2020, 10:29 a.m.