Michu Kom
2016-Jun-06 07:38 UTC
[R] Knitr R - how to draw plot exactly at place of plot function call in output document?
My R script run with Knitr generates a statistic summary of electrode pairs
accompanied with plots. The problem is that knitr does not render plots in
correct sections. In section for pair A knitr do not wait for plot and
start to evaluate code for output summary for pair B. So in section B knitr
places plot from section A among printed output summary for pair B.
My function analizePair calculates some statistics and print them out. I
call a ezPlot function inside analizePair function.
knitr::opts_chunk$set(fig.show = 'asis') # 'hold' option is not
proper
for my needs
for(pair in pairsLabels)
{
print("----------")
print("Analysing single pair of electrodes...")
print("----------")
print(pair)
analizePair(pairLabel = pair)
print("----------")
print("Analysing pair finished.")
print("----------")
}
I also tried to put Sys.sleep(2) after analizePair, but it do not solve the
problem.
How to force knitr/R to wait until plot is generated and put before
starting next section (next iteration of for loop) ?
[[alternative HTML version deleted]]
Ulrik Stervbo
2016-Jun-06 08:04 UTC
[R] Knitr R - how to draw plot exactly at place of plot function call in output document?
Hi Michu, What document type do you generate? I usually make just html and have no problems. If you create a pdf, please remember this is done through LaTeX and your problem could arise from the floats of LaTeX. For other output I have no idea. Hope this helps Ulrik Michu Kom <michu.kom at gmail.com> schrieb am Mo., 6. Juni 2016 09:41:> My R script run with Knitr generates a statistic summary of electrode pairs > accompanied with plots. The problem is that knitr does not render plots in > correct sections. In section for pair A knitr do not wait for plot and > start to evaluate code for output summary for pair B. So in section B knitr > places plot from section A among printed output summary for pair B. > > My function analizePair calculates some statistics and print them out. I > call a ezPlot function inside analizePair function. > > knitr::opts_chunk$set(fig.show = 'asis') # 'hold' option is not proper > for my needs > for(pair in pairsLabels) > { > print("----------") > print("Analysing single pair of electrodes...") > print("----------") > print(pair) > > analizePair(pairLabel = pair) > > print("----------") > print("Analysing pair finished.") > print("----------") > } > > I also tried to put Sys.sleep(2) after analizePair, but it do not solve the > problem. > > How to force knitr/R to wait until plot is generated and put before > starting next section (next iteration of for loop) ? > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >[[alternative HTML version deleted]]
Ulrik Stervbo
2016-Jun-07 05:51 UTC
[R] Knitr R - how to draw plot exactly at place of plot function call in output document?
Hi Michu, it is not I problem I am familiar with, sorry. Maybe someone else on this list or at the knirt google group can help you further. Best, Ulrik On Mon, 6 Jun 2016 at 10:36 Michu Kom <michu.kom at gmail.com> wrote:> Hello, > > HTML looks much nicer :) ... but still problem is not solved :/ still > having mixed sections and plots. > > Thank you for your advice, > Michu > > 2016-06-06 10:04 GMT+02:00 Ulrik Stervbo <ulrik.stervbo at gmail.com>: > >> Hi Michu, >> >> What document type do you generate? I usually make just html and have no >> problems. If you create a pdf, please remember this is done through LaTeX >> and your problem could arise from the floats of LaTeX. >> >> For other output I have no idea. >> >> Hope this helps >> Ulrik >> >> Michu Kom <michu.kom at gmail.com> schrieb am Mo., 6. Juni 2016 09:41: >> >>> My R script run with Knitr generates a statistic summary of electrode >>> pairs >>> accompanied with plots. The problem is that knitr does not render plots >>> in >>> correct sections. In section for pair A knitr do not wait for plot and >>> start to evaluate code for output summary for pair B. So in section B >>> knitr >>> places plot from section A among printed output summary for pair B. >>> >>> My function analizePair calculates some statistics and print them out. I >>> call a ezPlot function inside analizePair function. >>> >>> knitr::opts_chunk$set(fig.show = 'asis') # 'hold' option is not proper >>> for my needs >>> for(pair in pairsLabels) >>> { >>> print("----------") >>> print("Analysing single pair of electrodes...") >>> print("----------") >>> print(pair) >>> >>> analizePair(pairLabel = pair) >>> >>> print("----------") >>> print("Analysing pair finished.") >>> print("----------") >>> } >>> >>> I also tried to put Sys.sleep(2) after analizePair, but it do not solve >>> the >>> problem. >>> >>> How to force knitr/R to wait until plot is generated and put before >>> starting next section (next iteration of for loop) ? >>> >>> [[alternative HTML version deleted]] >>> >>> ______________________________________________ >>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >>> https://stat.ethz.ch/mailman/listinfo/r-help >>> PLEASE do read the posting guide >>> http://www.R-project.org/posting-guide.html >>> and provide commented, minimal, self-contained, reproducible code. >>> >> >[[alternative HTML version deleted]]
Jeff Newmiller
2016-Jun-08 16:59 UTC
[R] Knitr R - how to draw plot exactly at place of plot function call in output document?
I would echo the suggestion that the knitr Google group or stackexchange.com would be better than this list for this question. I also suggest that you look at http://yihui.name/knitr/demo/child/ and make a reproducible example if you decide to ask for more help in one of those forums. -- Sent from my phone. Please excuse my brevity. On June 6, 2016 10:51:36 PM PDT, Ulrik Stervbo <ulrik.stervbo at gmail.com> wrote:>Hi Michu, > >it is not I problem I am familiar with, sorry. Maybe someone else on >this >list or at the knirt google group can help you further. > >Best, >Ulrik > >On Mon, 6 Jun 2016 at 10:36 Michu Kom <michu.kom at gmail.com> wrote: > >> Hello, >> >> HTML looks much nicer :) ... but still problem is not solved :/ still >> having mixed sections and plots. >> >> Thank you for your advice, >> Michu >> >> 2016-06-06 10:04 GMT+02:00 Ulrik Stervbo <ulrik.stervbo at gmail.com>: >> >>> Hi Michu, >>> >>> What document type do you generate? I usually make just html and >have no >>> problems. If you create a pdf, please remember this is done through >LaTeX >>> and your problem could arise from the floats of LaTeX. >>> >>> For other output I have no idea. >>> >>> Hope this helps >>> Ulrik >>> >>> Michu Kom <michu.kom at gmail.com> schrieb am Mo., 6. Juni 2016 09:41: >>> >>>> My R script run with Knitr generates a statistic summary of >electrode >>>> pairs >>>> accompanied with plots. The problem is that knitr does not render >plots >>>> in >>>> correct sections. In section for pair A knitr do not wait for plot >and >>>> start to evaluate code for output summary for pair B. So in section >B >>>> knitr >>>> places plot from section A among printed output summary for pair B. >>>> >>>> My function analizePair calculates some statistics and print them >out. I >>>> call a ezPlot function inside analizePair function. >>>> >>>> knitr::opts_chunk$set(fig.show = 'asis') # 'hold' option is not >proper >>>> for my needs >>>> for(pair in pairsLabels) >>>> { >>>> print("----------") >>>> print("Analysing single pair of electrodes...") >>>> print("----------") >>>> print(pair) >>>> >>>> analizePair(pairLabel = pair) >>>> >>>> print("----------") >>>> print("Analysing pair finished.") >>>> print("----------") >>>> } >>>> >>>> I also tried to put Sys.sleep(2) after analizePair, but it do not >solve >>>> the >>>> problem. >>>> >>>> How to force knitr/R to wait until plot is generated and put before >>>> starting next section (next iteration of for loop) ? >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> ______________________________________________ >>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >>>> https://stat.ethz.ch/mailman/listinfo/r-help >>>> PLEASE do read the posting guide >>>> http://www.R-project.org/posting-guide.html >>>> and provide commented, minimal, self-contained, reproducible code. >>>> >>> >> > > [[alternative HTML version deleted]] > >______________________________________________ >R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >https://stat.ethz.ch/mailman/listinfo/r-help >PLEASE do read the posting guide >http://www.R-project.org/posting-guide.html >and provide commented, minimal, self-contained, reproducible code.[[alternative HTML version deleted]]