asdataframe: Conversion of a hyperSpec object into a data.frame or matrix...
In hyperSpec: Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)
Description
Usage
Arguments
Value
Author(s)
See Also
Examples
Description
Conversion of a hyperSpec object into a data.frame or matrix
as.data.frame returns x@data (as data.frame) as.matrix
returns the spectra matrix x@data$spc as matrix
as.wide.df converts the spectra matrix to a data.frame. The extra
data together with this data is returned. The column names of the spectra
matrix are retained (if they are numbers, without preceeding letters).
The data.frame returned by as.long.df is guaranteed to have columns
spc and .wavelength. If nwl (x) == 0 these columns
will be NA.
as.t.df produces a 'transposed' data.frame with columns containing the spectra.
Usage
1
2
3
4
5
6
7
8
9
10
11
## S3 method for class 'hyperSpec'
as.data.frame(x, row.names = TRUE, optional = NULL, ...)
## S3 method for class 'hyperSpec'
as.matrix(x, ...)
as.wide.df(x)
as.long.df(x, rownames = FALSE, wl.factor = FALSE, na.rm = TRUE)
as.t.df(x)
Arguments
x
a hyperSpec object
row.names
if TRUE, a column .row is created containing row names or row
indices if no rownames are set. If character vector, the rownames are set accordingly.
optional
ignored
...
ignored
rownames
should the rownames be in column .rownames of the
long-format data.frame?
wl.factor
should the wavelengths be returned as a factor (instead of
numeric)?
na.rm
if TRUE, rows where spc is not NA are deleted.
Value
x@data and x@data$spc (== x$spc == x [[]]), respectively.
as.wide.df returns a data.frame that consists of the extra data and
the spectra matrix converted to a data.frame. The spectra matrix is
expanded in place.
as.long.df returns the stacked or molten version of x@data. The
wavelengths are in column .wavelength.
as.t.df returns a data.frame similar to as.long.df, but each
spectrum in its own column. This is useful for exporting summary spectra,
see the example.
Author(s)
C. Beleites
See Also
and as.matrix
stack and melt or melt for
other functions producing long-format data.frames.
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
as.data.frame (chondro [1:3,, 600 ~ 620])
as.matrix (chondro [1:3,, 600 ~ 620])
lm (c ~ spc, data = flu [,,450])
as.wide.df (chondro [1:5,, 600 ~ 610])
summary (as.wide.df (chondro [1:5,, 600 ~ 610]))
as.long.df (flu [,, 405 ~ 410])
summary (as.long.df (flu [,, 405 ~ 410]))
summary (as.long.df (flu [,, 405 ~ 410], rownames = TRUE))
summary (as.long.df (flu [,, 405 ~ 410], wl.factor = TRUE))
df <- as.t.df (apply (chondro, 2, mean_pm_sd))
head (df)
if (require (ggplot2)){
ggplot (df, aes (x = .wavelength)) +
geom_ribbon (aes (ymin = mean.minus.sd, ymax = mean.plus.sd),
fill = "#00000040") +
geom_line (aes (y = mean))
}
Example output
Loading required package: lattice
Loading required package: grid
Loading required package: ggplot2
Package hyperSpec, version 0.99-20180627
To get started, try
vignette ("hyperspec")
package?hyperSpec
vignette (package = "hyperSpec")
If you use this package please cite it appropriately.
citation("hyperSpec")
will give you the correct reference.
The project homepage is http://hyperspec.r-forge.r-project.org
y x filename clusters spc.602 spc.606 spc.610 spc.614
1 -4.77 -11.55 rawdata/chondro.txt matrix 501.8194 504.8868 488.6323 466.1774
2 -4.77 -10.55 rawdata/chondro.txt matrix 500.4552 507.8126 489.4758 465.0506
3 -4.77 -9.55 rawdata/chondro.txt matrix 465.9614 474.6263 456.0324 436.6220
spc.618 .row
1 492.0016 1
2 490.5329 2
3 458.0576 3
602 606 610 614 618
[1,] 501.8194 504.8868 488.6323 466.1774 492.0016
[2,] 500.4552 507.8126 489.4758 465.0506 490.5329
[3,] 465.9614 474.6263 456.0324 436.6220 458.0576
Call:
lm(formula = c ~ spc, data = flu[, , 450])
Coefficients:
(Intercept) spc
0.0038493 0.0004407
y x filename clusters 602 606 610
1 -4.77 -11.55 rawdata/chondro.txt matrix 501.8194 504.8868 488.6323
2 -4.77 -10.55 rawdata/chondro.txt matrix 500.4552 507.8126 489.4758
3 -4.77 -9.55 rawdata/chondro.txt matrix 465.9614 474.6263 456.0324
4 -4.77 -8.55 rawdata/chondro.txt matrix 477.4786 481.7259 464.8207
5 -4.77 -7.55 rawdata/chondro.txt matrix 439.3865 445.0571 428.6620
y x filename clusters 602
Min. :-4.77 Min. :-11.55 Length:5 matrix:5 Min. :439.4
1st Qu.:-4.77 1st Qu.:-10.55 Class :character lacuna:0 1st Qu.:466.0
Median :-4.77 Median : -9.55 Mode :character cell :0 Median :477.5
Mean :-4.77 Mean : -9.55 Mean :477.0
3rd Qu.:-4.77 3rd Qu.: -8.55 3rd Qu.:500.5
Max. :-4.77 Max. : -7.55 Max. :501.8
606 610
Min. :445.1 Min. :428.7
1st Qu.:474.6 1st Qu.:456.0
Median :481.7 Median :464.8
Mean :482.8 Mean :465.5
3rd Qu.:504.9 3rd Qu.:488.6
Max. :507.8 Max. :489.5
.wavelength spc filename c
1 405.0 27.15000 rawdata/flu1.txt 0.05
2 405.0 66.80133 rawdata/flu2.txt 0.10
3 405.0 93.14433 rawdata/flu3.txt 0.15
4 405.0 130.66367 rawdata/flu4.txt 0.20
5 405.0 167.26667 rawdata/flu5.txt 0.25
6 405.0 198.43033 rawdata/flu6.txt 0.30
1.1 405.5 32.34467 rawdata/flu1.txt 0.05
2.1 405.5 63.71533 rawdata/flu2.txt 0.10
3.1 405.5 103.06767 rawdata/flu3.txt 0.15
4.1 405.5 139.99833 rawdata/flu4.txt 0.20
5.1 405.5 171.89833 rawdata/flu5.txt 0.25
6.1 405.5 209.45800 rawdata/flu6.txt 0.30
1.2 406.0 33.37867 rawdata/flu1.txt 0.05
2.2 406.0 66.71200 rawdata/flu2.txt 0.10
3.2 406.0 106.19367 rawdata/flu3.txt 0.15
4.2 406.0 143.79767 rawdata/flu4.txt 0.20
5.2 406.0 177.47067 rawdata/flu5.txt 0.25
6.2 406.0 215.78500 rawdata/flu6.txt 0.30
1.3 406.5 34.41933 rawdata/flu1.txt 0.05
2.3 406.5 69.58233 rawdata/flu2.txt 0.10
3.3 406.5 110.18633 rawdata/flu3.txt 0.15
4.3 406.5 148.42000 rawdata/flu4.txt 0.20
5.3 406.5 184.62467 rawdata/flu5.txt 0.25
6.3 406.5 224.58700 rawdata/flu6.txt 0.30
1.4 407.0 36.53133 rawdata/flu1.txt 0.05
2.4 407.0 72.52967 rawdata/flu2.txt 0.10
3.4 407.0 113.24867 rawdata/flu3.txt 0.15
4.4 407.0 152.13267 rawdata/flu4.txt 0.20
5.4 407.0 189.75233 rawdata/flu5.txt 0.25
6.4 407.0 232.52800 rawdata/flu6.txt 0.30
1.5 407.5 37.64767 rawdata/flu1.txt 0.05
2.5 407.5 74.55833 rawdata/flu2.txt 0.10
3.5 407.5 119.17300 rawdata/flu3.txt 0.15
4.5 407.5 159.31033 rawdata/flu4.txt 0.20
5.5 407.5 198.11533 rawdata/flu5.txt 0.25
6.5 407.5 240.77133 rawdata/flu6.txt 0.30
1.6 408.0 38.13700 rawdata/flu1.txt 0.05
2.6 408.0 77.04800 rawdata/flu2.txt 0.10
3.6 408.0 121.31333 rawdata/flu3.txt 0.15
4.6 408.0 165.05233 rawdata/flu4.txt 0.20
5.6 408.0 205.56267 rawdata/flu5.txt 0.25
6.6 408.0 248.04667 rawdata/flu6.txt 0.30
1.7 408.5 39.17700 rawdata/flu1.txt 0.05
2.7 408.5 80.25967 rawdata/flu2.txt 0.10
3.7 408.5 124.67533 rawdata/flu3.txt 0.15
4.7 408.5 168.68967 rawdata/flu4.txt 0.20
5.7 408.5 208.41933 rawdata/flu5.txt 0.25
6.7 408.5 256.89133 rawdata/flu6.txt 0.30
1.8 409.0 40.73567 rawdata/flu1.txt 0.05
2.8 409.0 82.53867 rawdata/flu2.txt 0.10
3.8 409.0 129.56867 rawdata/flu3.txt 0.15
4.8 409.0 175.45900 rawdata/flu4.txt 0.20
5.8 409.0 217.55267 rawdata/flu5.txt 0.25
6.8 409.0 262.73900 rawdata/flu6.txt 0.30
1.9 409.5 41.38133 rawdata/flu1.txt 0.05
2.9 409.5 84.49167 rawdata/flu2.txt 0.10
3.9 409.5 134.11733 rawdata/flu3.txt 0.15
4.9 409.5 181.58100 rawdata/flu4.txt 0.20
5.9 409.5 224.74633 rawdata/flu5.txt 0.25
6.9 409.5 270.27133 rawdata/flu6.txt 0.30
1.10 410.0 44.25133 rawdata/flu1.txt 0.05
2.10 410.0 88.15167 rawdata/flu2.txt 0.10
3.10 410.0 139.98667 rawdata/flu3.txt 0.15
4.10 410.0 185.69233 rawdata/flu4.txt 0.20
5.10 410.0 231.03567 rawdata/flu5.txt 0.25
6.10 410.0 281.82867 rawdata/flu6.txt 0.30
.wavelength spc filename c
Min. :405.0 Min. : 27.15 Length:66 Min. :0.050
1st Qu.:406.0 1st Qu.: 75.18 Class :character 1st Qu.:0.100
Median :407.5 Median :137.05 Mode :character Median :0.175
Mean :407.5 Mean :137.80 Mean :0.175
3rd Qu.:409.0 3rd Qu.:196.02 3rd Qu.:0.250
Max. :410.0 Max. :281.83 Max. :0.300
.rownames .wavelength spc filename c
1:11 Min. :405.0 Min. : 27.15 Length:66 Min. :0.050
2:11 1st Qu.:406.0 1st Qu.: 75.18 Class :character 1st Qu.:0.100
3:11 Median :407.5 Median :137.05 Mode :character Median :0.175
4:11 Mean :407.5 Mean :137.80 Mean :0.175
5:11 3rd Qu.:409.0 3rd Qu.:196.02 3rd Qu.:0.250
6:11 Max. :410.0 Max. :281.83 Max. :0.300
.wavelength spc filename c
405 : 6 Min. : 27.15 Length:66 Min. :0.050
405.5 : 6 1st Qu.: 75.18 Class :character 1st Qu.:0.100
406 : 6 Median :137.05 Mode :character Median :0.175
406.5 : 6 Mean :137.80 Mean :0.175
407 : 6 3rd Qu.:196.02 3rd Qu.:0.250
407.5 : 6 Max. :281.83 Max. :0.300
(Other):30
.wavelength mean.minus.sd mean mean.plus.sd
spc.602 602 297.8472 343.0481 388.2489
spc.606 606 300.0874 345.9178 391.7482
spc.610 610 290.3887 334.0423 377.6959
spc.614 614 280.1190 321.3384 362.5578
spc.618 618 297.8204 342.4266 387.0328
spc.622 622 314.7000 363.2688 411.8375
hyperSpec documentation built on May 2, 2019, 5:45 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Value Author(s) See Also Examples
Description
Conversion of a hyperSpec object into a data.frame or matrix
as.data.frame returns x@data (as data.frame) as.matrix
returns the spectra matrix x@data$spc as matrix
as.wide.df converts the spectra matrix to a data.frame. The extra
data together with this data is returned. The column names of the spectra
matrix are retained (if they are numbers, without preceeding letters).
The data.frame returned by as.long.df is guaranteed to have columns
spc and .wavelength. If nwl (x) == 0 these columns
will be NA.
as.t.df produces a 'transposed' data.frame with columns containing the spectra.
Usage
1 2 3 4 5 6 7 8 9 10 11 | ## S3 method for class 'hyperSpec'
as.data.frame(x, row.names = TRUE, optional = NULL, ...)
## S3 method for class 'hyperSpec'
as.matrix(x, ...)
as.wide.df(x)
as.long.df(x, rownames = FALSE, wl.factor = FALSE, na.rm = TRUE)
as.t.df(x)
|
Arguments
x |
a |
row.names |
if |
optional |
ignored |
... |
ignored |
rownames |
should the rownames be in column |
wl.factor |
should the wavelengths be returned as a factor (instead of numeric)? |
na.rm |
if |
Value
x@data and x@data$spc (== x$spc == x [[]]), respectively.
as.wide.df returns a data.frame that consists of the extra data and
the spectra matrix converted to a data.frame. The spectra matrix is
expanded in place.
as.long.df returns the stacked or molten version of x@data. The
wavelengths are in column .wavelength.
as.t.df returns a data.frame similar to as.long.df, but each
spectrum in its own column. This is useful for exporting summary spectra,
see the example.
Author(s)
C. Beleites
See Also
and as.matrix
stack and melt or melt for
other functions producing long-format data.frames.
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | as.data.frame (chondro [1:3,, 600 ~ 620])
as.matrix (chondro [1:3,, 600 ~ 620])
lm (c ~ spc, data = flu [,,450])
as.wide.df (chondro [1:5,, 600 ~ 610])
summary (as.wide.df (chondro [1:5,, 600 ~ 610]))
as.long.df (flu [,, 405 ~ 410])
summary (as.long.df (flu [,, 405 ~ 410]))
summary (as.long.df (flu [,, 405 ~ 410], rownames = TRUE))
summary (as.long.df (flu [,, 405 ~ 410], wl.factor = TRUE))
df <- as.t.df (apply (chondro, 2, mean_pm_sd))
head (df)
if (require (ggplot2)){
ggplot (df, aes (x = .wavelength)) +
geom_ribbon (aes (ymin = mean.minus.sd, ymax = mean.plus.sd),
fill = "#00000040") +
geom_line (aes (y = mean))
}
|
Example output
Loading required package: lattice
Loading required package: grid
Loading required package: ggplot2
Package hyperSpec, version 0.99-20180627
To get started, try
vignette ("hyperspec")
package?hyperSpec
vignette (package = "hyperSpec")
If you use this package please cite it appropriately.
citation("hyperSpec")
will give you the correct reference.
The project homepage is http://hyperspec.r-forge.r-project.org
y x filename clusters spc.602 spc.606 spc.610 spc.614
1 -4.77 -11.55 rawdata/chondro.txt matrix 501.8194 504.8868 488.6323 466.1774
2 -4.77 -10.55 rawdata/chondro.txt matrix 500.4552 507.8126 489.4758 465.0506
3 -4.77 -9.55 rawdata/chondro.txt matrix 465.9614 474.6263 456.0324 436.6220
spc.618 .row
1 492.0016 1
2 490.5329 2
3 458.0576 3
602 606 610 614 618
[1,] 501.8194 504.8868 488.6323 466.1774 492.0016
[2,] 500.4552 507.8126 489.4758 465.0506 490.5329
[3,] 465.9614 474.6263 456.0324 436.6220 458.0576
Call:
lm(formula = c ~ spc, data = flu[, , 450])
Coefficients:
(Intercept) spc
0.0038493 0.0004407
y x filename clusters 602 606 610
1 -4.77 -11.55 rawdata/chondro.txt matrix 501.8194 504.8868 488.6323
2 -4.77 -10.55 rawdata/chondro.txt matrix 500.4552 507.8126 489.4758
3 -4.77 -9.55 rawdata/chondro.txt matrix 465.9614 474.6263 456.0324
4 -4.77 -8.55 rawdata/chondro.txt matrix 477.4786 481.7259 464.8207
5 -4.77 -7.55 rawdata/chondro.txt matrix 439.3865 445.0571 428.6620
y x filename clusters 602
Min. :-4.77 Min. :-11.55 Length:5 matrix:5 Min. :439.4
1st Qu.:-4.77 1st Qu.:-10.55 Class :character lacuna:0 1st Qu.:466.0
Median :-4.77 Median : -9.55 Mode :character cell :0 Median :477.5
Mean :-4.77 Mean : -9.55 Mean :477.0
3rd Qu.:-4.77 3rd Qu.: -8.55 3rd Qu.:500.5
Max. :-4.77 Max. : -7.55 Max. :501.8
606 610
Min. :445.1 Min. :428.7
1st Qu.:474.6 1st Qu.:456.0
Median :481.7 Median :464.8
Mean :482.8 Mean :465.5
3rd Qu.:504.9 3rd Qu.:488.6
Max. :507.8 Max. :489.5
.wavelength spc filename c
1 405.0 27.15000 rawdata/flu1.txt 0.05
2 405.0 66.80133 rawdata/flu2.txt 0.10
3 405.0 93.14433 rawdata/flu3.txt 0.15
4 405.0 130.66367 rawdata/flu4.txt 0.20
5 405.0 167.26667 rawdata/flu5.txt 0.25
6 405.0 198.43033 rawdata/flu6.txt 0.30
1.1 405.5 32.34467 rawdata/flu1.txt 0.05
2.1 405.5 63.71533 rawdata/flu2.txt 0.10
3.1 405.5 103.06767 rawdata/flu3.txt 0.15
4.1 405.5 139.99833 rawdata/flu4.txt 0.20
5.1 405.5 171.89833 rawdata/flu5.txt 0.25
6.1 405.5 209.45800 rawdata/flu6.txt 0.30
1.2 406.0 33.37867 rawdata/flu1.txt 0.05
2.2 406.0 66.71200 rawdata/flu2.txt 0.10
3.2 406.0 106.19367 rawdata/flu3.txt 0.15
4.2 406.0 143.79767 rawdata/flu4.txt 0.20
5.2 406.0 177.47067 rawdata/flu5.txt 0.25
6.2 406.0 215.78500 rawdata/flu6.txt 0.30
1.3 406.5 34.41933 rawdata/flu1.txt 0.05
2.3 406.5 69.58233 rawdata/flu2.txt 0.10
3.3 406.5 110.18633 rawdata/flu3.txt 0.15
4.3 406.5 148.42000 rawdata/flu4.txt 0.20
5.3 406.5 184.62467 rawdata/flu5.txt 0.25
6.3 406.5 224.58700 rawdata/flu6.txt 0.30
1.4 407.0 36.53133 rawdata/flu1.txt 0.05
2.4 407.0 72.52967 rawdata/flu2.txt 0.10
3.4 407.0 113.24867 rawdata/flu3.txt 0.15
4.4 407.0 152.13267 rawdata/flu4.txt 0.20
5.4 407.0 189.75233 rawdata/flu5.txt 0.25
6.4 407.0 232.52800 rawdata/flu6.txt 0.30
1.5 407.5 37.64767 rawdata/flu1.txt 0.05
2.5 407.5 74.55833 rawdata/flu2.txt 0.10
3.5 407.5 119.17300 rawdata/flu3.txt 0.15
4.5 407.5 159.31033 rawdata/flu4.txt 0.20
5.5 407.5 198.11533 rawdata/flu5.txt 0.25
6.5 407.5 240.77133 rawdata/flu6.txt 0.30
1.6 408.0 38.13700 rawdata/flu1.txt 0.05
2.6 408.0 77.04800 rawdata/flu2.txt 0.10
3.6 408.0 121.31333 rawdata/flu3.txt 0.15
4.6 408.0 165.05233 rawdata/flu4.txt 0.20
5.6 408.0 205.56267 rawdata/flu5.txt 0.25
6.6 408.0 248.04667 rawdata/flu6.txt 0.30
1.7 408.5 39.17700 rawdata/flu1.txt 0.05
2.7 408.5 80.25967 rawdata/flu2.txt 0.10
3.7 408.5 124.67533 rawdata/flu3.txt 0.15
4.7 408.5 168.68967 rawdata/flu4.txt 0.20
5.7 408.5 208.41933 rawdata/flu5.txt 0.25
6.7 408.5 256.89133 rawdata/flu6.txt 0.30
1.8 409.0 40.73567 rawdata/flu1.txt 0.05
2.8 409.0 82.53867 rawdata/flu2.txt 0.10
3.8 409.0 129.56867 rawdata/flu3.txt 0.15
4.8 409.0 175.45900 rawdata/flu4.txt 0.20
5.8 409.0 217.55267 rawdata/flu5.txt 0.25
6.8 409.0 262.73900 rawdata/flu6.txt 0.30
1.9 409.5 41.38133 rawdata/flu1.txt 0.05
2.9 409.5 84.49167 rawdata/flu2.txt 0.10
3.9 409.5 134.11733 rawdata/flu3.txt 0.15
4.9 409.5 181.58100 rawdata/flu4.txt 0.20
5.9 409.5 224.74633 rawdata/flu5.txt 0.25
6.9 409.5 270.27133 rawdata/flu6.txt 0.30
1.10 410.0 44.25133 rawdata/flu1.txt 0.05
2.10 410.0 88.15167 rawdata/flu2.txt 0.10
3.10 410.0 139.98667 rawdata/flu3.txt 0.15
4.10 410.0 185.69233 rawdata/flu4.txt 0.20
5.10 410.0 231.03567 rawdata/flu5.txt 0.25
6.10 410.0 281.82867 rawdata/flu6.txt 0.30
.wavelength spc filename c
Min. :405.0 Min. : 27.15 Length:66 Min. :0.050
1st Qu.:406.0 1st Qu.: 75.18 Class :character 1st Qu.:0.100
Median :407.5 Median :137.05 Mode :character Median :0.175
Mean :407.5 Mean :137.80 Mean :0.175
3rd Qu.:409.0 3rd Qu.:196.02 3rd Qu.:0.250
Max. :410.0 Max. :281.83 Max. :0.300
.rownames .wavelength spc filename c
1:11 Min. :405.0 Min. : 27.15 Length:66 Min. :0.050
2:11 1st Qu.:406.0 1st Qu.: 75.18 Class :character 1st Qu.:0.100
3:11 Median :407.5 Median :137.05 Mode :character Median :0.175
4:11 Mean :407.5 Mean :137.80 Mean :0.175
5:11 3rd Qu.:409.0 3rd Qu.:196.02 3rd Qu.:0.250
6:11 Max. :410.0 Max. :281.83 Max. :0.300
.wavelength spc filename c
405 : 6 Min. : 27.15 Length:66 Min. :0.050
405.5 : 6 1st Qu.: 75.18 Class :character 1st Qu.:0.100
406 : 6 Median :137.05 Mode :character Median :0.175
406.5 : 6 Mean :137.80 Mean :0.175
407 : 6 3rd Qu.:196.02 3rd Qu.:0.250
407.5 : 6 Max. :281.83 Max. :0.300
(Other):30
.wavelength mean.minus.sd mean mean.plus.sd
spc.602 602 297.8472 343.0481 388.2489
spc.606 606 300.0874 345.9178 391.7482
spc.610 610 290.3887 334.0423 377.6959
spc.614 614 280.1190 321.3384 362.5578
spc.618 618 297.8204 342.4266 387.0328
spc.622 622 314.7000 363.2688 411.8375
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.