tgram {tgram}

Compute Tracheidograms

Description

Function to compute tracheidograms from microscopic measurements.

Usage

tgram(traq, val50 = 50, xlim = NULL, ylim = NULL, mw = 1, plotit = TRUE)

## S3 method for class 'tgram'
plot(x, xlim = NULL, ylim = NULL, colores = c("red", "green"),
      leyenda = c("lumen", "double wall"), lwd = 2,
      add = FALSE,traq.0 = TRUE, bg.legend = NULL, ...)

Arguments

traq

microscopic light profile. A vector with the light measurements or a data.frame or matrix with two columns. In this case, the first column contains pixel order (i.e. position along the x axis) and the second one contains the light (i.e. "y") lectures.

val50

"y-value" at wich measurements should be made.

mw

integer. Width of the rolling window to smooth the original data.

plotit

logical. should the original data and the computed tracheidogram be drawn?

xlim

extent of the x-axis. A vector of length 2.

ylim

extent of the y-axis. A vector of length 2.

x

an object of class tgram, resulting from tgram function.

colores

a vector of length 2, with the colors to draw the lumen and wall measurements, respectively.

leyenda

a vector of length 2 with the legend to appear in the plot. By default leyenda =c("lumen","double wall").

lwd

width of the lines in the legend.

add

logical. If TRUE, add to a current plot.

traq.0

logical. If TRUE, draw the original measurements.

bg.legend

background color for the legend.

...

additional graphical parameters.

Details

The purpouse of this fucntion is obtaining cell anatomical data from microscopic light measurements (see DeSoto et al. for details of data adquisition). The microscopic lectures are first smoothed with a rolling window (using function rollmean of package zoo, using the selected width mw. Then, the smoothed curve is "cut" at the treshold value val50 and the distances among the intersection points are computed. This provides an ordered sequence of lumen diameters (LD) and double wall thikness (DWT) measurements. From this sequence some other anatomical measurements are computed. Radial cell wall thickness is computed as CWT[t] = 1/2 * (DWT[t]/2 + DWT[t+1]/2) . Tracheid diameter is computed as TD[t] = DWT[t]/2 + LD[t] + DWT[t+1]/2.

Value

tgram returns an object of class tgram, bassically a list with

traq

original data.

traq0

if traq was a 2 column matrix, then traq0 returns the same object. If traq was a vector, traq0 returns a two column matrix (first column with pixel position and second with ligh lectures).

cut.points

two column matrix with the coordinates of the intersection of y = val50 and the smoothed curve.

what

vector indicating if the computed distances are of lumen (1) or double wall (2) .

distances

ordered sequence of the computed distances (both of lumen and double wall).

LD

ordered sequence of lumen diameters.

DWT

ordered sequence of double wall thickness.

mw

width of the rolling window employed to smooth the data.

CWT

ordered sequence of radial cell wall thikness'.

TD

ordered sequence of tracheid diameters.

LD_CWT_ratio

ordered sequence of LD/CWT ratio.

Author(s)

Marcelino de la Cruz Rot and Lucia DeSoto

References

DeSoto, L., De la Cruz, M. & Fonti, P. 2011. Intra-annual pattern of tracheid size in the Mediterranean Juniperus thurifera as indicator for seasonal water stress. Canadian Journal of Forest Research 41: 1280-1294.

Examples

data(traq.profile)

plot(tgram(traq.profile, mw=10),leyenda=c("lumen","double wall"),
        xlab="distance pixel", ylab="grey value",ylim=c(0,250),
        bg.legend="white")