I am currently trying to link an R-marking document with html (or pdf), where in a specific chunck I create several charts. I specify the titles through the argument fig.capin the chunck parameters with a vector of the same length as the number of graphs. However, for this to work, the cunck parameter messagemust be TRUE. The problem starts when the ggplot2 object is generated by a function in chucnk, and I want to apply a new fill with viridis::scale_fill_viridis. Which is good, but inevitably throws a message / warning that there is already a fill applied to the ggplot2 object, and that 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 include this in the output of my httml markdown. Usage suppressMessagesalso seems to suppress html (and pdf!) Titles. So my question is:is there a way to “disable” the existing scaling attribute to avoid generating this message ? In short, 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 saves signatures when the cunck option messages=F?
Yours faithfully,
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$set(echo = TRUE)
creategg <- function(x,plot=FALSE)
{
datnam <- names(x)
p <- ggplot(data=x,aes(x=x[,datnam[1]],
y=x[,datnam[2]],
fill=factor(x[,datnam[ncol(x)]]))) +
geom_bar(stat="identity") +
scale_fill_gdocs()
if(plot==TRUE){
print(p)
}
reslist <- list(inputdata=x,ggplotobj=p)
}
```
Actual report
```{r iriscars, fig.cap=c("plot with default fill","same plot with viridis fill"), echo=FALSE}
a <- creategg(iris,plot=TRUE)
a$ggplotobj + scale_fill_viridis(discrete=TRUE)
```
If necessary, my output is session_info ():
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
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