filterImages: Filter images

In lucyleeow/CellProfileR: Analyse Cell Morphology Data Generated By CellProfiler

Description

Filter poor quality images (using the powerloglog slope feature). plotFiltered plots the number of images filtered for each plate.

Usage

filterImages(df, num_IQR)

plotFiltered(filtered_df, num_images, annot, num_wells)

Arguments

df	Dataframe of raw CellProfiler data, where each row is one image NOT one well.
num_IQR	Number of IQR's below the 25 threshold.
filtered_df	The plate ID column from the filtered (for poor quality images) dataframe of CellProfiler data, as a dataframe or vector. E.g. if the plate ID column from the filtered dataframe filtered_df is called 'Metadata_Barcode', filtered_df[,'Metadata_Barcode'] OR filtered_df[['Metadata_Barcode']] can be used.
num_images	The number of images taken per well.
annot	Optional argument. The plate ID column from the annotation dataframe, as a vector or dataframe. E.g. if the plate ID column from the annot dataframe is called 'VCFG_Compound_Plate_ID', annot[,'VCFG_Compound_Plate_ID'] OR annot[['VCFG_Compound_Plate_ID']] can be used. If given, the number of filtered images (rows) will be calculated as: (number of used wells) * num_images - (number of images remaining after filtering). If not given, it will be assumed that all wells were used.
num_wells	Number of wells per plate.

Value

• filterImages returns the dataframe with poor quality images (rows) removed.

• plotFiltered creates a bar plot in the current graphics device.

Functions

• filterImages: Filter images (rows) with a powerloglog slope value below the threshold ('num_IQR' * IQR below the 25th percentile) in ANY channel.

• plotFiltered: Creates bar graph of the number of images filtered for each plate.

lucyleeow/CellProfileR documentation built on May 21, 2019, 2:30 a.m.