Plot several pictures with different size in a “fo

问题:

I am new to knitr and markdown and this is my first question asked. Maybe this question has a simple answer that I just can't find.

I have a for-loop, which creates 3 ggplots. The loop runs 300 to 400 times depending on the data input. I want to define the size of these 3 pictures as:

1st picture: width = 7, height = 3

2nd picture: width = 7, height = 3

3nd picture: width = 7, height = 12

So far I am using the following code:

```{r calc, echo=FALSE, warning=FALSE, message=FALSE, results='asis', fig.show='asis',fig.height=3}
for(x.PS in 1:length(trace.input)) 
{
# some data transformation by self-written functions

# create and save plot for the normalised version
ggp.PS.norm <- ggplot(print.PS.norm, aes(x = Time, y = Voltage, col = Pulse))
fig.PS.norm <- ggp.PS.norm + geom_line()

# create and save plot for the modified version
ggp.PS.smooth <- ggplot(print.PS.smooth, aes(x = Time, y = Voltage, col = Pulse))
fig.PS.smooth <- ggp.PS.smooth + geom_line()

# create and save plot for the modified version as facet grid
fig.PS.smooth.single <- ggp.PS.smooth + geom_line() + facet_grid(FigCol ~ FigRow)

print(fig.PS.norm)
print(fig.PS.smooth)
print(fig.PS.smooth.single)
}
```

In the end I hope to get one big PDF-file with 3 x 300 to 400 pictures

I hope this code is understandable even without any hard data.

best paj

回答1:

I don't know if this is kosher but here is one approach:

adapted from here

I'm using rmarkdown since that is what your question is in, but this could be adapted to latex

---
output: 
  html_document:
    css: ~/knitr.css
---

```{r, include=FALSE}
library(knitr)
opts_knit$set(progress = FALSE, verbose = FALSE)
opts_chunk$set(warning=FALSE, message=FALSE, echo=FALSE)

## this function is basically creating chunks within chunks, and then
## I use results='asis' so that the html image code is rendered 
kexpand <- function(ht, cap) {
  cat(knit(text = knit_expand(text = 
     sprintf("```{r %s, fig.height=%s, fig.cap='%s'}\n.pl\n```", cap, ht, cap)
)))}

library(ggplot2)
```


```{r, results='asis', fig.width=7}
for (ii in 1:2) {
  ## do some stuff

  cat('<br />')
  cat(paste0('Page', ii))

  ## all plots should be saved as .p1 and then use kexpand
  .pl <- qplot(mpg, wt, data=mtcars)
  kexpand(3, 'fig1')

  .pl <- qplot(mpg, wt, data=mtcars, colour=cyl)
  kexpand(3, 'fig2')

  .pl <- qplot(mpg, wt, data=mtcars, size=cyl)
  kexpand(7, 'fig3')

  cat('<br /><br />')
}
```

And this is my output

回答2:

you can print in a viewport of a specific size,

library(grid)
print_size = function(p, width=7, height=3) 
    print(p, vp=viewport(width=unit(width,"inch"), height=unit(height, "in")))

for(ii in 1:3)
   print_size(qplot(1,1), height = c(3,3,12)[ii])

回答3:

My own solution in the end:

At some point I call this chunk below in my parent script

<<test_child,results='asis'>>=
    knit.out <- NULL
    for(x.PS in 1:length(trace.input)) {
      knit.out <- c(knit.out,
                    knit_child("rawCAP_child_0-2.Rnw",
                           quiet = TRUE,
                           envir = globalenv()
                           )
      )
    }
    cat(paste(knit.out, collapse = '\n'))
@

The child script does some calculations and creates the figures like this

    <<,echo=FALSE>>=
# some functions creating the figures, for example the one below
ggp.PS.smooth <- ggplot(print.PS.smooth, aes(x = Time, y = Voltage, col = Pulse))
fig.PS.smooth <- ggp.PS.smooth + 
  geom_line() +
  scale_x_continuous(
    limits = c(len.1,len.total)
    ) + 
  scale_y_continuous(
    limits = c(-4,4)
    ) +
  labs(
    #title = "Data smoothed by a value of XX",
    x = "Time [sec.]",
    y = "Voltage [mV]")
@

These chunks print the figures with different heights, there is one table too.

<<,fig.height=2,fig.width=7,fig.align='center'>>=
print(fig.PS.smooth)
@

<<,echo=FALSE,results='asis',fig.align='center'>>=

xtable(table.PS.CAP.stat[c(2:5,13:16)],
       caption = "Statistics about all Pulses")
@

<<,fig.height=3,fig.width=7,fig.align='center'>>=
print(fig.PS.CAP)
@


<<,fig.height=12,fig.width=7,fig.align='center'>>=
print(fig.PS.smooth.single)
@

I am very happy with this solution, cause you can set almost everything without a workaround

For further help please look at Yihui's page, especially look here and maybe also here (this is stackoverflow). Yihui seems to be on stackoverflow too.

Best paj