viewOverlay

viewOverlay

Usage

viewOverlay(
  data,
  proc.img.dir,
  well.label,
  obj.label,
  obj.color = NULL,
  obj.col.pal = NULL,
  obj.shape = NULL,
  obj.shape.pal = NULL,
  text.anno = NULL,
  file = NULL
)

Arguments

data

A data frame output from modelSelection or any OF function from easyXpress. The dataframe should be filtered to contain only the wells to be plotted. Please Arrange the dataframe in the order that overlays are to be plotted.

proc.img.dir

A variable name in data that holds the full PATH to the directory holding processed images matching the data. The processed images must have the standard _overlay.png suffix and file name output from CellProfiler.

well.label

A variable name in data to display as a well label. For example, "Metadata_Well".

obj.label

A variable name in data to label objects by. For example, "model".

obj.color

Optional: A variable name in data to color objects by. The default is NULL.

obj.col.pal

Optional: A color palette for obj.labels. This is a vector of colors with names for each unique value in obj.color. NULL passes color values to obj.label.

obj.shape

Optional: A variable name in data to use for the shape of objects. The default is NULL.

obj.shape.pal

Optional: A shape palette for objects. This is a vector of shape values with names for each unique value in obj.shape. NULL passes shape values to obj.label.

text.anno

Optional: a variable name in data used to display text annotation at an object center. by default this value is shifted vertically to avoid plotting over object center.

file

Optional: The full path for saving output plot. Default is NULL which will just return the ggplot2 plot.

Value

A plot showing all the CellProfiler processed well overlays in data with objects annotated as desired.