Type: Package
Title: Densitometric Analysis of Thin-Layer Chromatography Plates
Version: 1.0
Date: 2016-01-03
Author: Ivan D. Pavicevic
Maintainer: Ivan D. Pavicevic <ivanp84@gmail.com>
Description: Densitometric evaluation of the photo-archived quantitative thin-layer chromatography (TLC) plates.
Depends: tiff, rgl, plot3D, graphics, grDevices, stats, utils
License: GPL-2
RoxygenNote: 5.0.1
Packaged: 2016-01-04 15:28:35 UTC; ivan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2016-01-04 17:46:53

Retention factor (Rf)

Description

Calculates Rf values of the spots based on the marked start and stop of the solvent path.

Usage

Rf(object, sf = F)

Arguments

object

S3 object of the working TLC

sf

Boolean, default FALSE - Start and Front should be marked. If TRUE, Start and Front were defined.

Value

Returns S3 object with new variables.

object$Rf_start

Location of the solvent start on the TLC plate

object$Rf_front

Location of the solvent end on the TLC plate

object$Rf

Rf values of the spots

Author(s)

Ivan D. Pavicevic, ivanp84@gmail.com

Examples

## Not run: 
#for more interactive variant; locate using mouse
object <- Rf(object, sf=TRUE)

## End(Not run)

Area vs. x-axis

Description

Function charts density plot of a single spot following x-axis.

Usage

areadens2D(object, spot = NULL, plot = TRUE, returndf = TRUE,
  ptype = "o", ...)

Arguments

object

S3 object of working TLC

spot

Number of the spot (counted left to right).

plot

Boolean, TRUE default and displays densitometric distribution.

returndf

Boolean, TRUE by default, returns data.frame with x and Area values.

ptype

Point type for the plot. Default "o" (Uses same values as type variable from plot function)

...

Additional parameters (for plot type function).

Value

Returns data.frame with x and Area values.

Author(s)

Ivan D. Pavicevic, ivanp84@gmail.com

Examples


# A test example
fname01 <- system.file("extdata", "test025to100sp.tiff", package="qtlc")
testTLC <- createTLC(fname01, RGB=FALSE)
print(testTLC)

# now we'll imitate interactive spot2D function,
# and create spots coordinates automatically,
# for interactive version run testTLC <- spot2D(testTLC)
testTLC$spots$x <- c(40.93354, 83.18687, 121.59899, 160.01111, 203.54485,
                     239.39616, 280.36909, 320.06161, 362.31494, 399.44666,
                     439.13919, 480.11211, 518.52423, 559.49716, 599.18969)
testTLC$spots$y <- c(198.3160, 198.3160, 199.2833, 198.3160, 198.3160,
                     198.3160, 198.3160, 198.3160, 197.3487, 198.3160,
                     199.2833, 198.3160, 199.2833, 199.2833, 199.2833)

testTLC <- select2D(testTLC, 30, 30)
testTLC <- matrices2D(testTLC)
testTLC <- summat2D(testTLC)

# and now test the areadens2D for each spot
par(mfrow=c(3,3))
for(i in 1:15) {
areadens2D(testTLC, spot=i, ptype="l")
}

Shows areadens2D plus background noise as segmented line

Description

Plots area-denses of the spot and background.

Usage

areadensnoisecompare2D(object, spot = NULL, plot = TRUE, returndf = TRUE,
  ptype = "o", ...)

Arguments

object

S3 object of working TLC

spot

Number of the spot (counted left to right).

plot

Boolean, TRUE default and displays densitometric distribution.

returndf

Boolean, TRUE by default, returns data.frame with x and Area values.

ptype

Point type for the plot. Default "o" (Uses same values as type variable from plot function)

...

Additional parameters (for plot type function).

Value

Returns data.frame with x and Area values.

Author(s)

Ivan D. Pavicevic, ivanp84@gmail.com

Examples

## Not run: 
#see areadens2D first
areadensnoisecompare2D(object, spot=3, ptype="l")

## End(Not run)

Creates TLC S3 object

Description

Create matrix from TLC image

Usage

createTLC(ttiff, turnv = TRUE, ...)

Arguments

ttiff

File name of the TIFF image with scanned TLC plate.

turnv

Boolean value determines to turn vertically data in the matrix. TRUE generates turned image which is useful for Cartesian coordinates, because without turning the coordinate system begins in the left corner of the monithor and rises left and down.

...

Additional parameters for TIFF image manipulation.

Value

An object of class qtlc, that contains TLC matrix and descriptions. The object contains:

file_name

File name of of the TIFF image from which the TLC matrix was created.

mat

TLC matrix (or matrices if intensities Red, Green and Blue channels are not combined.)

spots

Coordinates of marked spots (using function spot2D).

Author(s)

Ivan D. Pavicevic, ivanp84@gmail.com

Examples

#Creates test matrix.
# RGB channels stay separated, or
# intensities are combined.
fname01 <- system.file("extdata", "testTIFF.tiff", package="qtlc")
testTLC <- createTLC(fname01, RGB=TRUE)
print(testTLC)

Creates spots matrices

Description

Using spots locations and areas this function creates a matrix for each spot.

Usage

matrices2D(object, ...)

Arguments

object

S3 object of working TLC

...

Additional graphical parameters. (At this time just experimental)

Value

Returns S3 object with new variable object$spot_matrices which is a three dimensional matrix (width, height, and pixel intensity values).

Author(s)

Ivan D. Pavicevic, ivanp84@gmail.com

Examples

## Not run: 
#just makes spot matrices for selected spots of the object
object <- matrices2D(object)

## End(Not run)

Converts matrix back to image

Description

Using S3 qtlc object, extracts the matrix and converts to image plot.

Usage

matrixtoimage(object, show = TRUE, bkg = "thistle", axes = FALSE,
  xlab = "", ylab = "", ...)

Arguments

object

S3 object of working TLC.

show

Boolean, default TRUE. Shows the plot of the image.

bkg

If show is TRUE, then defines background color. Default is "thistle".

axes

Boolean, default FALSE. Shows x,y axes if TRUE.

xlab

Label of the x-axis.

ylab

Label of the y-axis.

...

Additional graphical parameters.

Value

Returns image as matrix suitable for plot, or other graphics functinos.

Author(s)

Ivan D. Pavicevic, ivanp84@gmail.com

Examples

# Converts test image to matrix,
# then matrix back to image.
fname01 <- system.file("extdata", "testTIFF.tiff", package="qtlc")
testTLC <- createTLC(fname01, RGB=FALSE)
print(testTLC)
matrixtoimage(testTLC, bkg="white")

Polynomial estimation of the image noise.

Description

Estimation, and noise removal using polynomial model.

Usage

noisepoly2D(object, gd = 20, power = 5, col = "green")

Arguments

object

S3 object of the working TLC

gd

Defines position of the center of the rectangular samples of the image background (above or bellow located spots).

power

Order of the polynome.

col

Color of the borders of the rectangles for bkg samples.

Value

Returns S3 object with new variables.

object$noise_mat

The 3D matrix (width, height, number of spots)

object$noise_fit

Linear model for the polynomial fit

object$noisefit_spot_sums

Sums of the noise samples areas

Author(s)

Ivan D. Pavicevic, ivanp84@gmail.com

Examples

## Not run: 
#object is a tlc with 14 spots, and selection 50x80(wxh)
object <- noisepoly2D(object, gd=80, power=13)

## End(Not run)

Normalization of the matrix values

Description

Experimental function. Normalize matrix data.

Usage

normalize2D(mat)

Arguments

mat

Matrix of the TLC plate.

Value

Normalized matrix.

Author(s)

Ivan D. Pavicevic, ivanp84@gmail.com

Examples

## Not run: 
new_mat <- normalize2D(mat)

## End(Not run)

Converting TIFF to matrix.

Description

Mostly internal function used by createTLC function. Additional parameters from createTLC goes there (RGB, comb).

Usage

picmatrixTIFF(ff, RGB = TRUE, comb = c(0.3, 0.59, 0.11))

Arguments

ff

TIFF file

RGB

Boolean, TRUE - keeps Red, Green and Blue intensities as three matrices. FALSE - using comb to combine intensities.

comb

Vector, combines intensities according to luma. A vector containing three values for R, G and B conversion.

Value

Returns combined intensities matrix, or separated R, G, B matrices.

Author(s)

Ivan D. Pavicevic, ivanp84@gmail.com

Examples

## Not run: 
#Internal function used by createTLC(...)

## End(Not run)

Print Method for qtlc object

Description

Redefined print method.

Usage

## S3 method for class 'qtlc'
print(x, ...)

Arguments

x

S3 object of the working TLC.

...

Additional parameters for the print method

Value

Prints qtlc S3 object details

Author(s)

Ivan D. Pavicevic, ivanp84@gmail.com

Examples

## Not run: 
print(object)

## End(Not run)

Summary method for qtlc S3 object

Description

Summary method for qtlc S3 object

Usage

## S3 method for class 'summary.qtlc'
print(x, ...)

Arguments

x

S3 object of the working TLC.

...

Additional parameters.

Value

Summary.

Author(s)

Ivan D. Pavicevic, ivanp84@gmail.com

Examples

## Not run: 
summary(object)

## End(Not run)

Rotate vertically

Description

Rotate entire matrix vertically. Mostly internal function.

Usage

rotatev(mat)

Arguments

mat

The matrix.

Value

Rotated matrix.

Author(s)

Ivan D. Pavicevic, ivanp84@gmail.com

Examples

## Not run: 
new_mat <- rotatev(mat)

## End(Not run)

Internal function used by showtlc3D

Description

Internal function used by showtlc3D

Usage

s3D(mat, ogl, grey, ...)

Arguments

mat

Matrix with x,y,Intensity dimensions

ogl

If TLC 3D plot use OpenGL library for fast and interactive 3D plot. (This functionality is based on the rgl package.) Otherwise the function is based on the plot3D package.

grey

Boolean, if TRUE, then tlc is greyscaled. Default value is FALSE.

...

Additional graphics parameters.

Value

None.

Author(s)

Ivan D. Pavicevic, ivanp84@gmail.com

Examples

## Not run: 
#Internal function.

## End(Not run)

Selects spots areas

Description

Based on the located spots centers (manualy with mouse and function spot2D) this function defines spots areas.

Usage

select2D(object, w, h, col = "white")

Arguments

object

S3 object of the working TLC.

w

Width of the spot area.

h

Height of the spot area.

col

Color of the border (default white)

Value

Return S3 object with new variable object$mat_cell which is list with "w" and "h" values.

Author(s)

Ivan D. Pavicevic, ivanp84@gmail.com

Examples

## Not run: 
select2D(object, 80, 50)

## End(Not run)

Shows Rf on the plot

Description

Shows prior analysed Rf on the new plot of the 2D matrix.

Usage

showRf(object, col = "green", adjust = NULL, cex = 0.6)

Arguments

object

S3 object of the working TLC

col

Color of the lines.

adjust

Adjustment for the space of the text. Default value is usualy just OK.

cex

A zoom factor for the text.

Value

None.

Author(s)

Ivan D. Pavicevic, ivanp84@gmail.com

Examples

## Not run: 
showRf(object)

## End(Not run)

Show TLC matrix as 2D plot

Description

Using TLC matrix width, height, and intensity parameters this function plot 2D heatmap of the TLC matrix.

Usage

showtlc2D(object, ...)

Arguments

object

S3 object of the working TLC

...

Additional parameters

Value

None

Author(s)

Ivan D. Pavicevic, ivanp84@gmail.com

Examples

## Not run: 
showtlc2D(object)

## End(Not run)

Show TLC matrix as 2D plot

Description

Using TLC matrix width, height, and intensity parameters this function plot 2D heatmap of the TLC matrix.

Usage

## S3 method for class 'qtlc'
showtlc2D(object, specific = NULL, RGB = "", main = "",
  correction = TRUE, grey = FALSE, ...)

Arguments

object

S3 object of the working TLC

specific

Matrix of the specific spot (from object$spot_matrices)

RGB

RGB matrices (if they are present in the object) are separated on the plot. Values of the RGB = "R", or "G", or "B".

main

Main title of the plot.

correction

Experimental option, currently not in use.

grey

Boolean, if TRUE, then TLC plate is greyscaled. Default value is FALSE.

...

Additional graphical parameters

Value

None

Author(s)

Ivan D. Pavicevic, ivanp84@gmail.com

Examples

## Not run: 
showtlc2D(object, specific=object$spot_matrices[3], grey=TRUE)

## End(Not run)

Shows 3D plot of the TLC matrix.

Description

The function uses TLC matrix width, height and intensity values to make 3D plot.

Usage

showtlc3D(object, spot = NULL, ogl = FALSE, RGB = NULL, grey = FALSE,
  ...)

Arguments

object

S3 object of the working TLC.

spot

If the specific spot should be represented in 3D, but not entire TLC matrix. (Spot number is given as value, and spots are counted from left to right.)

ogl

If TLC 3D plot use OpenGL library for fast and interactive 3D plot. (This functionality is based on the rgl package.) Otherwise the function is based on the plot3D package.

RGB

If RGB matrices are present in the object, choose between R, G, or B.

grey

Boolean, if TRUE, then tlc is greyscaled. Default value is FALSE.

...

Additional graphics parameters.

Value

None.

Author(s)

Ivan D. Pavicevic, ivanp84@gmail.com

Examples

# Tests 3D plot of the entire matrix
fname01 <- system.file("extdata", "test025to100sp.tiff", package="qtlc")
testTLC <- createTLC(fname01, RGB=FALSE)

# now we'll imitate interactive spot2D function,
# and create spots coordinates automatically,
# for interactive version run testTLC <- spot2D(testTLC)
testTLC$spots$x <- c(40.93354, 83.18687, 121.59899, 160.01111, 203.54485,
                     239.39616, 280.36909, 320.06161, 362.31494, 399.44666,
                     439.13919, 480.11211, 518.52423, 559.49716, 599.18969)
testTLC$spots$y <- c(198.3160, 198.3160, 199.2833, 198.3160, 198.3160,
                     198.3160, 198.3160, 198.3160, 197.3487, 198.3160,
                     199.2833, 198.3160, 199.2833, 199.2833, 199.2833)

testTLC <- select2D(testTLC, 30, 30)
testTLC <- matrices2D(testTLC)
testTLC <- summat2D(testTLC)

# 3D without OpenGL, shows only spot 13
showtlc3D(testTLC, spot=13, ogl=FALSE, grey=FALSE)
# without openGL and greyscaled
showtlc3D(testTLC, spot=13, ogl=FALSE, grey=TRUE)
#openGL showtime
showtlc3D(testTLC, spot=13, ogl=TRUE)

Locate spots manually.

Description

The function should be used after 2D TLC matrix was plotted. After function call, the user should manually locate centers of the spots using mouse. (Left click for locate, right for the end of the process.)

Usage

spot2D(object, col = "white", ...)

Arguments

object

S3 object of the working TLC.

col

Color of the spot locator (default is white)

...

Additional parameters.

Value

S3 object with 'object$spots' added.

Author(s)

Ivan D. Pavicevic, ivanp84@gmail.com

Examples

## Not run: 
print(object)
object <- spot2D(object)

## End(Not run)

Summary method for qtlc S3 object

Description

Summary method for qtlc S3 object

Usage

## S3 method for class 'qtlc'
summary(object, ...)

Arguments

object

S3 object of the working TLC.

...

Additional parameters for the summary method

Value

Summary.

Author(s)

Ivan D. Pavicevic, ivanp84@gmail.com

Examples

## Not run: 
summary(object)

## End(Not run)

Summarize matrices

Description

The function summarize matrices areas of the located spot matrices.

Usage

summat2D(object)

Arguments

object

S3 object of working TLC

Value

Returns S3 object with new values object$spot_sums.

Author(s)

Ivan D. Pavicevic, ivanp84@gmail.com

Examples

# This interactive example shows the most
# common usage of the qtlc library.
fname01 <- system.file("extdata", "test025to100sp.tiff", package="qtlc")
testTLC <- createTLC(fname01, RGB=FALSE)
print(testTLC)

# now using mouse select the spots with testTLC <- spot2D(testTLC)
# but, for automatic tests, we'll imitate that step...
testTLC$spots$x <- c(40.93354, 83.18687, 121.59899, 160.01111, 203.54485,
                     239.39616, 280.36909, 320.06161, 362.31494, 399.44666,
                     439.13919, 480.11211, 518.52423, 559.49716, 599.18969)
testTLC$spots$y <- c(198.3160, 198.3160, 199.2833, 198.3160, 198.3160,
                     198.3160, 198.3160, 198.3160, 197.3487, 198.3160,
                     199.2833, 198.3160, 199.2833, 199.2833, 199.2833)

# and now the select2D selects 30x30 pixels areas around spots
testTLC <- select2D(testTLC, 30, 30)

# forming spots matrices
testTLC <- matrices2D(testTLC)

# and finaly sumarizing spots areas
testTLC <- summat2D(testTLC)

#eventually we'll examine the linear model
C <- rep(c(0.25, 1, 6.25, 25, 100), each=3) #imaginative concentrations
#now creates data frame with values
testTLC.df <- data.frame(C, testTLC$spot_sums)
names(testTLC.df) <- c("Concentration", "Signal")
# now the linear model
testTLC.lm <- with(testTLC.df, lm(Signal ~ Concentration))
# and finaly the plot
plot(testTLC.df)
abline(testTLC.lm)
summary(testTLC.lm)