Description Usage Arguments Details Value See Also Examples
Make a slice by slice display of a data.frame, a Carto3D
or a MRIaggr
object.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ## S4 method for signature 'data.frame'
multiplot(object, contrast = NULL, num = NULL,
index1 = NULL, index2 = NULL, index3 = NULL,
col = NULL, pch = NULL ,xlim = NULL, ylim = NULL, filename = "multiplot",...)
## S4 method for signature 'Carto3D'
multiplot(object, num = NULL,
col=NULL, pch = NULL, xlim = NULL, ylim = NULL,
filename = "multiplot",...)
## S4 method for signature 'MRIaggr'
multiplot(object, param, num = NULL,
index1 = NULL, index2 = NULL, index3 = NULL,
midplane = FALSE, col = NULL, pch = NULL, xlim = NULL, ylim = NULL,
filename = "multiplot", ...)
|
object |
an object of class |
param |
the contrast parameter to display. character. REQUIRED. |
contrast |
the intensities to display. numerical vector or |
num |
the slices to display. numeric vector or |
index1,index2,index3 |
the coordinates of additionnal points to display. data.frame or list or |
midplane |
should the mid-sagittal plan be displayed ? logical. |
col |
the color with which the observations will be displayed. character vector or |
pch |
the symbol with which the observations will be displayed. positive integer or |
xlim |
the x limits of the plot. numeric vector of size 2 or |
ylim |
the y limits of the plot. numeric vector of size 2 or |
filename |
the name of the file used to export the plot. character. |
... |
additional arguments to be passed to |
ARGUMENTS:
Information about the num
argument can be found in the details section of initNum
.
Information about the index1
, index2
and index3
arguments can be found in the details section of initIndex
(argument index
).
Information about the ...
can be found in the documentation of the optionsMRIaggr
function.
Invisible, return a list containing :
breaks.plot | the breaks used to display the images. |
palette.plot | the palette used to display the images. |
breaks.legend | the breaks used to display the legend. character. |
palette.legend | the palette used to display the legend. character. |
quantiles.legend | the quantiles used to display the legend. character. |
plotLesion3D
for a 3D plot of the lesion.
slices3d
of the misc3d package for a more interactive 3D plot.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 | #### 1- data.frame ####
## simulate
n <- 10
Y <- rnorm(n^2)
## display
multiplot(object = data.frame(expand.grid(1:n,1:n),1),
contrast = Y, window = FALSE)
## load a MRIaggr object
data(MRIaggr.Pat1_red, package = "MRIaggr")
## select data
data <- selectContrast(MRIaggr.Pat1_red,
param = c("DWI_t0","TTP_t0","MTT_t0","MASK_T2_FLAIR_t2"),
hemisphere = "lesion", coords = TRUE)
## fit model
glm.1 <- glm(MASK_T2_FLAIR_t2 ~ DWI_t0 + TTP_t0 + MTT_t0, data = data,
family = binomial(link = "logit"))
## display fitted values
multiplot(object = data[,c("i","j","k")],
contrast = predict(glm.1, type = "response"), window = FALSE)
## display residuals
multiplot(object = data[,c("i","j","k")], num = 3,
contrast = predict(glm.1, type = "response"), window = FALSE,
index1 = list(coords = data[data$MASK_T2_FLAIR_t2,c("i","j","k")], outline = TRUE)
)
#### 2- carto3D ####
## load NIFTI files and convert them to carto3D
path.Pat1 <- system.file("nifti", package = "MRIaggr")
nifti.Pat1_TTP_t0 <- readMRI(file.path(path.Pat1, "TTP_t0"), format = "nifti")
Carto3D.Pat1_TTP_t0 <- constCarto3D(nifti.Pat1_TTP_t0, identifier = "Pat1", param = "TTP_t0")
## display
multiplot(Carto3D.Pat1_TTP_t0)
## Not run:
multiplot(Carto3D.Pat1_TTP_t0, num = 1:2)
multiplot(Carto3D.Pat1_TTP_t0, num = 1:2, axes = FALSE)
multiplot(Carto3D.Pat1_TTP_t0, num = 1:2, axes = FALSE, legend = FALSE)
multiplot(Carto3D.Pat1_TTP_t0, num = 1:2, axes = FALSE, legend = FALSE,
main = "", num.main = FALSE)
multiplot(Carto3D.Pat1_TTP_t0, num = 1:2, axes = FALSE, main = "", num.main = FALSE,
palette = "gray.colors", breaks = seq(0,100))
## End(Not run)
#### 3- MRIaggr ####
## load a MRIaggr object
data(MRIaggr.Pat1_red, package = "MRIaggr")
# display 3 slices
multiplot(MRIaggr.Pat1_red, param = "DWI_t0",
num = 1:3)
## Not run:
# display 3 slices with no axes and white background
multiplot(MRIaggr.Pat1_red, param = "DWI_t0",
num = 1:3, axes = FALSE, bg = "white")
# remove the legend
multiplot(MRIaggr.Pat1_red, param = "DWI_t0",
num = 1:3, legend = FALSE)
## End(Not run)
## display an set of points
# using a binary parameter stored in the object
multiplot(MRIaggr.Pat1_red, param = "DWI_t0",
num = 1:3, index1 = list(coords = "MASK_DWI_t0")
)
## Not run:
# customize the display of the points
multiplot(MRIaggr.Pat1_red, param = "DWI_t0",
num = 1:3, index1 = list(coords = "MASK_DWI_t0", col = "pink", pch = 14)
)
# display only the edges of the set
multiplot(MRIaggr.Pat1_red, param = "DWI_t0", num = 3, legend = FALSE,
index1 = list(coords = "MASK_DWI_t0", outline = TRUE)
)
# specify the index of points using coordinates
coordsIndex <- data.frame(i = c(40,60), j = c(80,100), k = c(3,3))
multiplot(MRIaggr.Pat1_red, param = "DWI_t0", num = 3, legend = FALSE,
index2 = list(coords = coordsIndex, col = "black", pch = 15, cex = 4)
)
# various possibilities for the display
multiplot(MRIaggr.Pat1_red, num = 1:3, param = "DWI_t0",
legend = FALSE, window = FALSE)
multiplot(MRIaggr.Pat1_red, num = 1:3, param = "DWI_t0",
legend = TRUE, window = FALSE)
multiplot(MRIaggr.Pat1_red, num = 1:3, param = "DWI_t0",
legend = NULL, window = FALSE)
multiplot(MRIaggr.Pat1_red, num = 1:3, param = "DWI_t0",
legend = "only", window = FALSE)
## End(Not run)
|
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