问题
I am currently trying to knit an R markdown document to html (or pdf) where in a certain chunck I generate multiple plots. I specify the captions through the fig.cap argument in the chunck options with a vector of the same length as the number of plots. However, for this to work the cunck option message has to be TRUE.
The issue starts when a ggplot2 object is generated by a function in the chucnk and I want to apply a new fill with viridis::scale_fill_viridis. Which is fine, but inevitably throws a message/warning that there is already a fill applied to the ggplot2 object and that the viridis will replace it (Scale for 'fill' is already present. Adding another scale for 'fill', which will replace the existing scale). I do not want to get this into the output of my markdown html. Using suppressMessages apparently also suppresses the html (and pdf!) captions.
So my question is: is there a way to "unset" the existing scales attribute to avoid this message being generated? Short from that my only other option would be to dive into the code that generated the object in the first place. Or: is there a way that knitr preserves captions when the cunck option messages=F?
Kind regards,
FM
A minimal working example would be the following code in an R markdown document:
---
title: "SOtest"
author: "FM Kerckhof"
date: "1/9/2017"
output: html_document
---
```{r setup, include=FALSE}
library(ggplot2)
library(ggthemes)
library(viridis)
knitr::opts_chunk$set(echo = TRUE)
#### custom function ####
creategg <- function(x,plot=FALSE)
{
datnam <- names(x)
p <- ggplot(data=x,aes(x=x[,datnam[1]],
y=x[,datnam[2]],
fill=factor(x[,datnam[ncol(x)]]))) +
geom_bar(stat="identity") +
scale_fill_gdocs()
if(plot==TRUE){
print(p)
}
reslist <- list(inputdata=x,ggplotobj=p)
}
```
## Lorem ipsum
Actual report
```{r iriscars, fig.cap=c("plot with default fill","same plot with viridis fill"), echo=FALSE}
a <- creategg(iris,plot=TRUE)
a$ggplotobj + scale_fill_viridis(discrete=TRUE)
```
If relevant, my session_info() output is:
Session info -------------------------------------------------------------------------------------------
setting value
version R version 3.4.1 (2017-06-30)
system x86_64, linux-gnu
ui RStudio (1.0.153)
language (EN)
collate en_US.UTF-8
tz Europe/Brussels
date 2017-09-01
Packages -----------------------------------------------------------------------------------------------
package * version date source
ade4 1.7-8 2017-08-09 CRAN (R 3.4.1)
ape 4.1 2017-02-14 CRAN (R 3.3.2)
assertthat * 0.2.0 2017-04-11 CRAN (R 3.3.3)
backports 1.1.0 2017-05-22 CRAN (R 3.4.0)
base * 3.4.1 2017-07-08 local
bindr 0.1 2016-11-13 CRAN (R 3.4.0)
bindrcpp 0.2 2017-06-17 CRAN (R 3.4.0)
Biobase * 2.36.2 2017-05-09 Bioconductor
BiocGenerics * 0.22.0 2017-05-04 Bioconductor
biomformat 1.4.0 2017-05-04 Bioconductor
Biostrings 2.44.2 2017-07-24 Bioconductor
bitops 1.0-6 2013-08-17 CRAN (R 3.2.4)
caTools 1.17.1 2014-09-10 CRAN (R 3.2.4)
cluster 2.0.6 2017-03-16 CRAN (R 3.4.0)
codetools 0.2-15 2016-10-05 CRAN (R 3.3.1)
colorspace 1.3-2 2016-12-14 CRAN (R 3.3.2)
compiler 3.4.1 2017-07-08 local
data.table 1.10.4 2017-02-01 CRAN (R 3.3.2)
datasets * 3.4.1 2017-07-08 local
devtools * 1.13.3 2017-08-02 CRAN (R 3.4.1)
digest 0.6.12 2017-01-27 CRAN (R 3.3.2)
dplyr * 0.7.2 2017-07-20 CRAN (R 3.4.1)
evaluate 0.10.1 2017-06-24 CRAN (R 3.4.0)
extrafont * 0.17 2014-12-08 CRAN (R 3.4.0)
extrafontdb 1.0 2012-06-11 CRAN (R 3.4.0)
foreach 1.4.3 2015-10-13 CRAN (R 3.2.4)
gdata 2.18.0 2017-06-06 CRAN (R 3.4.0)
ggplot2 * 2.2.1 2016-12-30 CRAN (R 3.3.2)
ggthemes * 3.4.0 2017-02-19 CRAN (R 3.3.2)
glue 1.1.1 2017-06-21 CRAN (R 3.4.0)
gplots * 3.0.1 2016-03-30 CRAN (R 3.2.4)
graphics * 3.4.1 2017-07-08 local
grDevices * 3.4.1 2017-07-08 local
grid 3.4.1 2017-07-08 local
gridExtra 2.2.1 2016-02-29 CRAN (R 3.3.1)
gtable 0.2.0 2016-02-26 CRAN (R 3.2.4)
gtools * 3.5.0 2015-05-29 CRAN (R 3.2.4)
htmltools 0.3.6 2017-04-28 CRAN (R 3.4.0)
igraph 1.1.2 2017-07-21 CRAN (R 3.4.1)
IRanges 2.10.2 2017-06-01 Bioconductor
iterators 1.0.8 2015-10-13 CRAN (R 3.2.4)
jsonlite 1.5 2017-06-01 CRAN (R 3.4.0)
KernSmooth 2.23-15 2015-06-29 CRAN (R 3.4.0)
knitr 1.17 2017-08-10 CRAN (R 3.4.1)
labeling 0.3 2014-08-23 CRAN (R 3.2.4)
lattice * 0.20-35 2017-03-25 CRAN (R 3.3.3)
lazyeval 0.2.0 2016-06-12 CRAN (R 3.3.1)
magrittr 1.5 2014-11-22 CRAN (R 3.2.4)
MASS 7.3-47 2017-04-21 CRAN (R 3.4.0)
Matrix 1.2-11 2017-08-16 CRAN (R 3.4.1)
memoise 1.1.0 2017-04-21 CRAN (R 3.4.0)
methods * 3.4.1 2017-07-08 local
mgcv 1.8-19 2017-08-29 CRAN (R 3.4.1)
multtest 2.32.0 2017-05-04 Bioconductor
munsell 0.4.3 2016-02-13 CRAN (R 3.2.4)
nlme 3.1-131 2017-02-06 CRAN (R 3.3.2)
parallel * 3.4.1 2017-07-08 local
permute * 0.9-4 2016-09-09 CRAN (R 3.3.1)
phyloseq 1.20.0 2017-05-04 Bioconductor
pkgconfig 2.0.1 2017-03-21 CRAN (R 3.4.0)
plyr * 1.8.4 2016-06-08 CRAN (R 3.3.1)
R6 2.2.2 2017-06-17 CRAN (R 3.4.0)
Rcpp 0.12.12 2017-07-15 CRAN (R 3.4.1)
reshape2 * 1.4.2 2016-10-22 CRAN (R 3.3.2)
rhdf5 2.20.0 2017-05-04 Bioconductor
rlang 0.1.2 2017-08-09 CRAN (R 3.4.1)
rmarkdown 1.6 2017-06-15 CRAN (R 3.4.0)
rprojroot 1.2 2017-01-16 CRAN (R 3.3.2)
Rttf2pt1 1.3.4 2016-05-19 CRAN (R 3.4.0)
S4Vectors 0.14.3 2017-06-06 Bioconductor
scales 0.5.0 2017-08-24 CRAN (R 3.4.1)
splines 3.4.1 2017-07-08 local
stats * 3.4.1 2017-07-08 local
stats4 3.4.1 2017-07-08 local
stringi 1.1.5 2017-04-07 CRAN (R 3.3.3)
stringr 1.2.0 2017-02-18 CRAN (R 3.3.2)
survival 2.41-3 2017-04-04 CRAN (R 3.3.3)
tibble 1.3.4 2017-08-22 CRAN (R 3.4.1)
tools 3.4.1 2017-07-08 local
utils * 3.4.1 2017-07-08 local
vegan * 2.4-4 2017-08-24 CRAN (R 3.4.1)
viridis * 0.4.0 2017-03-27 CRAN (R 3.4.1)
viridisLite * 0.2.0 2017-03-24 CRAN (R 3.3.3)
withr 2.0.0 2017-07-28 CRAN (R 3.4.1)
XVector 0.16.0 2017-05-04 Bioconductor
yaml 2.1.14 2016-11-12 CRAN (R 3.3.2)
zlibbioc 1.22.0 2017-05-04 Bioconductor
回答1:
Take a look at a ggplot object, here p:
str(p)
There's a lot of sub-structure. Take a look at p$scales. It's a ScalesList. The following might help you:
i <- which(sapply(p$scales$scales, function(x) 'fill' %in% x$aesthetics))
p$scales$scales[[i]] <- NULL
来源：https://stackoverflow.com/questions/45998396/unset-existing-scale-fill-discrete-in-ggplot2-or-suppress-message-for-new-scale