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X11 X11 1 pdf
2
3
4
Theguresdisplayedarethedevicenumberswhichmustbeusedtochange
theactivedevice.Toknowwhatistheactivedevice:
> dev.cur()
pdf
4
andtochangetheactivedevice:
> dev.set(3)
X11
3
Thefunction dev.off()closes s a a device: : bydefaultthe e active deviceis
closed, otherwise this s is the onewhichnumberis given n as s argument to o the
function.Rthendisplaysthenumberofthenewactivedevice:
> dev.off(2)
X11
3
> dev.off()
pdf
4
TwospecicfeaturesoftheWindowsversionofRareworthmentioning:
aWindowsMetaledevicecanbeopenwiththefunctionwin.metafile,and
amenu\History"displayed whenthegraphicalwindowis s selectedallowing
recordingofallgraphsdrawnduringasession(bydefault,therecordingsystem
iso,theuserswitchesitonbyclickingon\Recording"inthismenu).
4.1.2
Partitioning a graphic
Thefunctionsplit.screenpartitionstheactivegraphicaldevice. Forexam-
ple:
> split.screen(c(1, 2))
divides thedevice into o twoparts s whichcanbeselected d withscreen(1)or
screen(2); erase.screen() ) deletes s the last drawn graph. . A A part t of the
devicecanitselfbedividedwithsplit.screen()leadingtothepossibilityto
makecomplexarrangements.
Thesefunctionsareincompatiblewithothers(suchaslayoutorcoplot)
andmust not beusedwithmultiplegraphicaldevices. . Theiruseshouldbe
limited,forinstance,tographicalexplorationofdata.
Thefunctionlayoutpartitionstheactivegraphicwindowinseveralparts
wherethegraphswillbedisplayedsuccessively. Itsmainargumentisama-
trixwithintegernumbersindicatingthenumbersofthe\sub-windows". For
example,todividethedeviceintofourequalparts:
37
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> layout(matrix(1:4, 2, , 2))
Itisofcoursepossibletocreatethismatrixpreviouslyallowingtobetter
visualizehowthedeviceisdivided:
> mat <- matrix(1:4, 2, , 2)
> mat
[,1] [,2]
[1,]
1
3
[2,]
2
4
> layout(mat)
Toactuallyvisualizethepartitioncreated,onecanusethefunctionlayout.show
withthenumberofsub-windowsas argument(here4). . Inthis s example,we
willhave:
> layout.show(4)
1
2
3
4
Thefollowingexamplesshowsomeofthepossibilitiesoeredbylayout().
> layout(matrix(1:6, 3, , 2))
> layout.show(6)
1
2
3
4
5
6
> layout(matrix(1:6, 2, , 3))
> layout.show(6)
1
2
3
4
5
6
> m <- matrix(c(1:3, 3), 2, 2)
> layout(m)
> layout.show(3)
1
2
3
Inalltheseexamples,wehavenotusedtheoptionbyrowofmatrix(),the
sub-windowsarethusnumberedcolumn-wise;onecanjustspecifymatrix(...,
byrow=TRUE)sothatthesub-windowsarenumberedrow-wise. Thenumbers
38
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inthematrixmayalsobegiveninanyorder,forexample,matrix(c(2, 1,
4, 3), 2, 2).
Bydefault,layout()partitionsthedevicewithregularheightsandwidths:
thiscanbemodiedwiththeoptionswidthsandheights.Thesedimensions
aregivenrelatively
12
. Examples:
> m <- matrix(1:4, 2, , 2)
> layout(m, widths=c(1, 3),
heights=c(3, 1))
> layout.show(4)
1
2
3
4
> m <- matrix(c(1,1,2,1),2,2)
> layout(m, widths=c(2, 1),
heights=c(1, 2))
> layout.show(2)
1
2
Finally,thenumbersinthematrixcanincludezerosgivingthepossibility
tomakecomplex(orevenesoterical)partitions.
> m <- matrix(0:3, 2, , 2)
> layout(m, c(1, 3), c(1, 3))
> layout.show(3)
1
2
3
> m <- matrix(scan(), , 5, , 5)
1: 0 0 0 0 3 3 3 3 3 1 1 1 3 3 3 3
11: 0 0 0 3 3 3 3 3 0 2 2 2 2 0 5
21: 4 4 2 2 2 0 0 5
26:
Read 25 5 items
> layout(m)
> layout.show(5)
1
2
3
4
5
12
Theycanbegivenincentimetres,see?layout.
39
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4.2 Graphicalfunctions
Hereisanoverviewofthehigh-levelgraphicalfunctionsinR.
plot(x)
plotofthevaluesof x(onthey-axis)orderedonthex-axis
plot(x, y)
bivariateplotof x(onthex-axis)andy(onthey-axis)
sunflowerplot(x,
y)
id.butthepointswithsimilarcoordinatesaredrawnasa ower
whichpetalnumberrepresentsthenumberofpoints
pie(x)
circularpie-chart
boxplot(x)
\box-and-whiskers"plot
stripchart(x)
plotofthevaluesofxonaline(analternativetoboxplot()for
smallsamplesizes)
coplot(x~y j j z)
bivariateplotof xandyforeachvalue(orintervalofvalues)of
z
interaction.plot
(f1, f2, y)
iff1andf2arefactors,plotsthemeansofy(onthey-axis)with
respecttothevaluesof f1(onthex-axis)andof f f2(dierent
curves);theoption funallows tochoose thesummarystatistic
of y(bydefaultfun=mean)
matplot(x,y)
bivariateplotoftherstcolumnof xvs.therstoneof y,the
secondoneof xvs.thesecondoneof y,etc.
dotchart(x)
if xis s adataframe, plots aCleveland dot plot (stacked plots
line-by-lineandcolumn-by-column)
fourfoldplot(x)
visualizes,withquartersofcircles,theassociation between two
dichotomous variables for dierent populations (xmust be an
array with h dim=c(2, , 2, k), or r a a matrix with h dim=c(2, , 2) if
k=1)
assocplot(x)
Cohen{Friendly graph showing g the e deviations from indepen-
dence of rows s and d columns in a a twodimensional contingency
table
mosaicplot(x)
‘mosaic’graphoftheresidualsfromalog-linearregressionofa
contingencytable
pairs(x)
ifxisamatrixoradataframe,drawsallpossiblebivariateplots
betweenthecolumnsof x
plot.ts(x)
if xisanobject ofclass "ts",plotof xwithrespecttotime,x
maybemultivariatebuttheseriesmusthavethesamefrequency
anddates
ts.plot(x)
id.but if f xis s multivariatethe series may havedierent dates
andmusthavethesamefrequency
hist(x)
histogramofthefrequenciesof x
barplot(x)
histogramofthevaluesof x
qqnorm(x)
quantilesofxwithrespecttothevaluesexpectedunderanormal
law
qqplot(x, y)
quantilesofywithrespecttothequantilesof x
contour(x, y, , z)
contour plot t (data a are interpolated to draw w the curves), x
and y must t be vectors s and z must t be a a matrix so that
dim(z)=c(length(x), length(y))(xandymaybeomitted)
filled.contour (x,
y, z)
id.buttheareasbetweenthecontoursarecoloured,andalegend
ofthecoloursisdrawnaswell
image(x, y, z)
id.buttheactualdataarerepresentedwithcolours
persp(x, y, z)
id.butinperspective
stars(x)
if xisamatrix oradataframe,draws agraph withsegments
orastarwhereeach row of xis represented byastarand the
columnsarethelengthsofthesegments
40
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symbols(x, y, , ...)
draws, at t the e coordinates s given n by x x and y, symbols (circles,
squares, rectangles, , stars, , thermometres s or r \boxplots") ) which
sizes,colours,etc,arespeciedbysupplementaryarguments
termplot(mod.obj)
plotofthe(partial)eectsofaregressionmodel(mod.obj)
Foreachfunction,the optionsmay befoundwiththeon-linehelpinR.
Some ofthese options areidenticalforseveralgraphicalfunctions; here are
themainones(withtheirpossibledefaultvalues):
add=FALSE
if TRUE E superposes the e plot on n the previous s one (if f it
exists)
axes=TRUE
if FALSEdoesnotdrawtheaxesandthebox
type="p"
species thetypeofplot, , "p": : points, , "l": : lines, , "b":
pointsconnectedbylines,"o": id.butthelinesareover
the points, "h": : vertical l lines,"s": : steps,thedata a are
representedbythetopoftheverticallines,"S": id.but
the data are representedby the bottom of the vertical
lines
xlim=, ylim= = species s the lowerandupperlimits oftheaxes, , for r ex-
amplewithxlim=c(1, 10)orxlim=range(x)
xlab=, ylab= = annotatestheaxes,mustbevariablesofmodecharacter
main=
maintitle,mustbeavariableofmodecharacter
sub=
sub-title(writteninasmallerfont)
4.3 Low-levelplottingcommands
Rhasasetofgraphicalfunctionswhichaectanalreadyexistinggraph:they
arecalledlow-levelplottingcommands. Herearethemainones:
points(x, y)
addspoints(theoptiontype=canbeused)
lines(x, y)
id.butwithlines
text(x, y, labels,
...)
addstextgivenbylabelsatcoordinates(x,y);atypicaluseis:
plot(x, y, type="n"); text(x, y, names)
mtext(text,
side=3, line=0,
...)
adds text given bytext t in n the margin n specied d by side(see
axis()below);linespeciesthelinefromtheplottingarea
segments(x0, y0,
x1, y1)
drawslinesfrompoints(x0,y0)topoints(x1,y1)
arrows(x0, y0,
x1, y1, angle= 30,
code=2)
id.witharrows atpoints(x0,y0)if f code=2,atpoints(x1,y1) ) if
code=1, or both h if f code=3; angle e controls s the anglefrom m the
shaftofthearrowtotheedgeofthearrowhead
abline(a,b)
drawsalineofslopebandintercepta
abline(h=y)
drawsahorizontallineatordinatey
abline(v=x)
drawsaverticallineatabcissax
abline(lm.obj)
drawstheregressionlinegivenbylm.obj(seesection5)
41
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rect(x1, y1, x2,
y2)
draws arectanglewhichleft,right, bottom,andtop limitsare
x1,x2,y1,andy2,respectively
polygon(x, y)
drawsapolygonlinkingthepointswithcoordinatesgivenbyx
andy
legend(x, y,
legend)
adds the legend at t the e point (x,y) with the symbols s given n by
legend
title()
addsatitleandoptionallyasub-title
axis(side, vect)
addsanaxisatthebottom(side=1),ontheleft(2),atthetop
(3), or on n the right (4); ; vect(optional) ) gives the abcissa a (or
ordinates)wheretick-marksaredrawn
box()
addsaboxaroundthecurrentplot
rug(x)
drawsthedataxonthex-axisassmallverticallines
locator(n,
type="n", ...)
returnsthecoordinates(x;y)aftertheuserhasclicked ntimes
ontheplot withthemouse; alsodrawssymbols (type="p") or
lines (type="l") with respect to optional l graphic parameters
(...);bydefaultnothingisdrawn(type="n")
Notethepossibilitytoaddmathematicalexpressionsonaplotwithtext(x,
y, expression(...)),wherethefunctionexpressiontransformsits s argu-
mentinamathematicalequation.Forexample,
> text(x, y, expression(p == over(1, 1+e^-(beta*x+alpha))))
willdisplay, on the plot, the following equationat t the point of coordinates
(x;y):
p=
1
1+e (
x
+)
Toincludeinanexpressionavariablewecanusethefunctionssubstitute
andas.expression;for exampletoincludeavalueof R
2
(previously com-
putedandstoredinanobjectnamedRsquared):
> text(x, y, as.expression(substitute(R^2==r, , list(r=Rsquared))))
willdisplayontheplotatthepointofcoordinates(x;y):
R
2
=0:9856298
Todisplayonlythreedecimals,wecanmodifythecodeasfollows:
> text(x, y, as.expression(substitute(R^2==r,
+
list(r=round(Rsquared, 3)))))
willdisplay:
R
2
=0:986
Finally,towritetheRinitalics:
> text(x, y, as.expression(substitute(italic(R)^2==r,
+
list(r=round(Rsquared, 3)))))
R
2
=0:986
42
4.4 Graphicalparameters
Inadditiontolow-levelplottingcommands,thepresentationofgraphicscan
beimprovedwithgraphicalparameters. Theycanbeusedeither r asoptions
ofgraphicfunctions(butitdoesnotworkforall),orwiththefunctionparto
change permanentlythegraphicalparameters, i.e.thesubsequent plotswill
bedrawnwithrespecttotheparametersspeciedbytheuser. Forinstance,
thefollowingcommand:
> par(bg="yellow")
will result t inallsubsequent plots drawn with ayellow background. . There
are73graphicalparameters,someofthemhavevery similarfunctions. . The
exhaustive list t of f these parameters can be read with ?par; I will limit the
followingtabletothemostusualones.
adj
controls textjustication with respecttotheleft border of the text sothat
0isleft-justied,0.5is centred,1isright-justied,values>1movethetext
furthertotheleft,andnegativevaluesfurthertotheright;if twovaluesare
given(e.g.,c(0, 0))thesecondonecontrolsverticaljusticationwithrespect
tothetextbaseline
bg
speciesthecolour ofthebackground(e.g., bg="red", bg="blue";thelistof
the657availablecoloursisdisplayedwithcolors())
bty
controls the e type of f box x drawn n around the plot, , allowed d values are: : "o",
"l","7","c","u"ou"]"(theboxlooks likethecorrespondingcharacter);if
bty="n"theboxisnotdrawn
cex
avaluecontrollingthesizeoftextsandsymbolswithrespecttothedefault;the
followingparametershavethesamecontrolfornumbersontheaxes,cex.axis,
theaxislabels,cex.lab,thetitle,cex.main,andthesub-title,cex.sub
col
controls the colour of symbols; ; as s for cex there are: : col.axis, , col.lab,
col.main,col.sub
font
an integer which controls the styleof text (1: : normal,2: : italics,3: : bold, , 4:
bolditalics);asforcexthereare:font.axis,font.lab,font.main,font.sub
las
anintegerwhichcontrolstheorientation oftheaxislabels(0: : paralleltothe
axes,1: horizontal,2: perpendiculartotheaxes,3:vertical)
lty
controls thetypeof lines,can bean integer (1: : solid, , 2: : dashed, , 3: : dotted,
4: dotdash, , 5: : longdash, , 6: : twodash), , or astringof up p to o eight t characters
(between "0"and "9") which species alternativelythelength, , in n points or
pixels,ofthedrawnelementsandtheblanks,forexamplelty="44"willhave
thesameeetthanlty=2
lwd
anumericwhichcontrolsthewidthoflines
mar
avectorof4numericvalueswhichcontrolthespacebetweentheaxesandthe
border of the graph of theform m c(bottom, , left, top, , right),thedefault
valuesarec(5.1, 4.1, , 4.1, , 2.1)
mfcol
avectoroftheformc(nr,nc)which partitionsthegraphicwindowasama-
trix of f nr r lines s and nc c columns, , the e plots s are e then drawn n in columns s (see
section4.1.2)
mfrow
id.buttheplotsarethendrawninline(seesection 4.1.2)
pch
controlsthetypeofsymbol,eitheranintegerbetween1and25,oranysingle
characterwithin""(Fig.2)
ps
anintegerwhichcontrolsthesizeinpointsoftextsandsymbols
43
*
?
X
a
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
"*"
"?" "." " "X" " "a"
Figure2: TheplottingsymbolsinR(pch=1:25). Thecolourswereobtained
withtheoptionscol="blue", bg="yellow",thesecondoptionhasaneect
onlyforthesymbols 21{25. . Anycharacter r canbeused(pch="*","?",".",
...).
pty
acharacter whichspeciesthetypeof theplottingregion,"s": : square,"m":
maximal
tck
avalue which species thelengthof tick-marks on theaxesas afraction of
thesmallestofthewidthorheightoftheplot;if tck=1agridisdrawn
tcl
id.butasafractionoftheheightofalineoftext(bydefaulttcl=-0.5)
xaxt
if xaxt="n" " the x-axis is set but t not t drawn (useful l in conjunction with
axis(side=1, ...))
yaxt
if yaxt="n" " the y-axis is set but t not t drawn (useful in conjunction with
axis(side=2, ...))
4.5 Apracticalexample
In order r to o illustrate R’s s graphical l functionalities, let t us consider r a simple
example of a bivariate graphof 10 pairs of random variates. . These e values
weregeneratedwith:
> x <- rnorm(10)
> y <- rnorm(10)
Thewantedgraphwillbeobtainedwithplot();onewilltypethecommand:
> plot(x, y)
and the e graph h will be plotted d on n the e active graphical l device. . The e result
is shown n on Fig. 3. By y default, , R R makes s graphs s in n an n \intelligent" " way:
44
−0.5
0.0
0.5
1.0
−1.0
−0.5
0.0
0.5
x
y
Figure3: Thefunctionplotusedwithoutoptions.
thespaces betweentick-marks ontheaxes,theplacementoflabels,etc,are
calculatedsothattheresultinggraphisasintelligibleaspossible.
Theusermay,nevertheless,changethewayagraphispresented,forin-
stance, to conformto a pre-denededitorial style, , or r to o give it a personal
touchforatalk. Thesimplestwaytochangethepresentationofagraphisto
addoptionswhichwillmodifythedefaultarguments. Inourexample,wecan
modifysignicantlythegureinthefollowingway:
plot(x, y, , xlab="Ten n random values", ylab="Ten other values",
xlim=c(-2, 2), ylim=c(-2, 2), pch=22, col="red",
bg="yellow", bty="l", , tcl=0.4,
main="How to customize a plot with h R", , las=1, cex=1.5)
The result is onFig. 4. Let t us detaileach of the used options. . First,
xlabandylabchangetheaxislabelswhich,bydefault,werethenamesofthe
variables. Then,xlimandylimallowustodenethelimitsonbothaxes
13
.
The graphicalparameter pch is usedhere as an option: : pch=22species s a
squarewhichcontourandbackgroundcoloursmaybedierentandaregiven
by, respectively, , col l and d bg. . The e table e of f graphical parameters gives s the
meaningofthemodicationsdonebybty,tcl,lasandcex. Finally,atitle
isaddedwiththeoptionmain.
Thegraphicalparametersandthelow-levelplottingfunctionsallowusto
gofurtherinthepresentationofagraph. Aswehaveseenpreviously,some
graphicalparameterscannotbepassedasargumentstoafunctionlikeplot.
13
Bydefault,Radds4%oneachsideoftheaxislimit. Thisbehaviourmaybealteredby
settingthegraphicalparametersxaxs="i"andyaxs="i"(theycan bepassedasoptionsto
plot()).
45
−2
−1
0
1
2
−2
−1
0
1
2
How to customize a plot with R
Ten random values
Ten other values
Figure4: Thefunctionplotusedwithoptions.
Wewillnowmodifysomeoftheseparameterswithpar(),itisthusnecessary
to type several commands. . Whenthe e graphicalparameters are changed,it
is useful l to save their initial values beforehand to be able e to o restore them
afterwards.HerearethecommandsusedtoobtainFig.5.
opar <- - par()
par(bg="lightyellow", col.axis="blue", , mar=c(4, 4, 2.5, , 0.25))
plot(x, y, , xlab="Ten n random values", ylab="Ten other values",
xlim=c(-2, 2), ylim=c(-2, 2), pch=22, col="red", bg="yellow",
bty="l", tcl=-.25, las=1, cex=1.5)
title("How to o customize a plot with R (bis)", font.main=3, , adj=1)
par(opar)
Letusdetailtheactionsresultingfromthesecommands.First,thedefault
graphicalparametersarecopiedinalistcalledhereopar. Threeparameters
willbethenmodied: bgforthecolourofthebackground,col.axisforthe
colourofthenumbersontheaxes,andmarforthesizesofthemarginsaround
theplottingregion.ThegraphisdrawninanearlysimilarwaytoFig.4.The
modicationsofthemarginsallowedtousethespacearoundtheplottingarea.
Thetitlehereisaddedwiththelow-levelplottingfunctiontitlewhichallows
togivesomeparametersasargumentswithoutalteringtherestofthegraph.
Finally,theinitialgraphicalparametersarerestoredwiththelastcommand.
Now, total l control! ! OnFig. 5, R still determines s a a few things s suchas
thenumberoftickmarksontheaxes,orthespacebetweenthetitleandthe
plottingarea. Wewillseenowhowtototallycontrolthepresentationofthe
graph. The e approachusedhereis toplota \blank"graphwithplot(...,
type="n"),thentoaddpoints,axes,labels,etc,withlow-levelplottingfunc-
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