No method for merging theme into element_rect

cloejoly · September 20, 2021, 5:46pm

Hi Community !
I'm having an issue but I'm not sure what is the problem...
Here is my script (modified from an other old one) :

# Function to get the probability into a whole matrix not half, here is Spearman you can change it to Kendall or Pearson
cor.prob.all <- function (X, dfr = nrow(X) - 2) {
  R <- cor(X, use="pairwise.complete.obs",method="spearman")
  r2 <- R^2
  Fstat <- r2 * dfr/(1 - r2)
  R<- 1 - pf(Fstat, 1, dfr)
  R[row(R) == col(R)] <- NA
  R
}
# Change matrices to dataframes
nba = Dataf
nbar<- as.data.frame(cor(nba[1:ncol(nba)]),method="spearman") # to a dataframe for r^2
nbap<- as.data.frame(cor.prob.all(nba[1:ncol(nba)])) # to a dataframe for p values
# Reset rownames
nbar <- data.frame(row=rownames(nbar),nbar) # create a column called "row" 
rownames(nbar) <- NULL
nbap <- data.frame(row=rownames(nbap),nbap) # create a column called "row" 
rownames(nbap) <- NULL
# Melt
library(reshape2)
??Rcpp_precious_remove
nbar.m <- melt(nbar)
nbap.m <- melt(nbap)
# Classify (you can classify differently for nbar and for nbap also)         
nbar.m$value2<-cut(nbar.m$value,breaks=c(-1,-0.75,-0.5,-0.25,0,0.25,0.5,0.75,1),include.lowest=TRUE, label=c("(-0.75,-1)","(-0.5,-0.75)","(-0.25,-0.5)","(0,-0.25)","(0,0.25)","(0.25,0.5)","(0.5,0.75)","(0.75,1)")) # the label for the legend
nbap.m$value2<-cut(nbap.m$value,breaks=c(-Inf, 0.001, 0.01, 0.05),label=c("***", "** ", "*  ")) 
nbar.m<-cbind.data.frame(nbar.m,nbap.m$value,nbap.m$value2) # adding the p value and its cut to the first dataset of R coefficients
names(nbar.m)[4]<-paste("valuep") # change the column names of the dataframe 
names(nbar.m)[4]<-paste("signif.")
nbar.m$row <- factor(nbar.m$row, levels=rev(unique(as.character(nbar.m$variable)))) # reorder the variable factor
# Plotting the matrix correlation heatmap
# Set options for a blank panel
po.nopanel <-list(theme(panel.background=theme_void(),panel.grid.minor=theme_void(),panel.grid.major=theme_void()))
pa<-ggplot(nbar.m, aes(row, variable)) +
  geom_tile(aes(fill=value2),colour="white") +
  scale_fill_brewer(palette = "RdYlGn",name="Correlation")+ # RColorBrewer package
  #theme(axis.text.x=theme_text(angle=-90))+
  po.nopanel
pa

Everything works fine until this answer appears... :

> pa # check the first plot
Error : No method for merging theme into element_rect

I don't understand what is the probleme here.
I think it is because the script is old and the function (which one ?) probably doesn't exist anymore. So how should I edit my new script ?

Thanks a lot,
Cloé

xvalda · September 20, 2021, 6:03pm

Hi Cloé, do you mind sharing the data? Or a subset of it? Just to know what Dataf looks like.

nirgrahamuk · September 21, 2021, 8:57am

I believe you have simply confused the use of theme_void with element_blank.

example of your issue:

library(tidyverse)

po.nopanel <-list(theme(panel.background=theme_void(),panel.grid.minor=theme_void(),panel.grid.major=theme_void()))

pa<-ggplot(iris, aes(Sepal.Length, Petal.Length)) +
  geom_tile(aes(fill=Species),colour="white") +
  scale_fill_brewer(palette = "RdYlGn",name="Correlation")  + 
  po.nopanel

pa

solution:

library(tidyverse)

po.nopanel <-list(theme(panel.background=element_blank(),panel.grid.minor=element_blank(),panel.grid.major=element_blank()))

pa<-ggplot(iris, aes(Sepal.Length, Petal.Length)) +
  geom_tile(aes(fill=Species),colour="white") +
  scale_fill_brewer(palette = "RdYlGn",name="Correlation")  + 
  po.nopanel

pa

cloejoly · September 21, 2021, 5:29pm

Here is my Dataf :

	CRI	DS	Ascaris	Coccidias	Strongyles	partners	age
Berthe	1,270642202	13,83366893	0	0	0	16	17
Bulle	0,879781421	71,49250489	3,5	3	7	16	17
Georgika	1,064102564	14,0998227	0,666666667	5,666666667	6,333333333	16	12
Gindia	1,278431373	39,13119004	0	2	10,33333333	15	11
Hillary	1,296089385	3,242757601	9,25	1,5	1,75	13	10
Himalaya	1,19375	-2,087402026	0	0,5	3	5	10
Holliday	1,197115385	33,39066188	0	0,666666667	12,66666667	14	10
Iena	1,054621849	46,83488485	0,5	0,5	3,5	14	9
Inca	1,089171975	-5,118630703	0	3,5	16,5	13	9
Isidore	1,159322034	-0,756084512	0	0,5	24,5	16	10
Kakie	1,278688525	8,940206386	1,5	6,5	11	7	20
Orphee	1,180327869	14,05813226	0	2	5	8	4
Pamela	1,358552632	-10,7906219	0	0,5	14	7	2
Priska	1,313829787	-33,34665086	3	1,5	11	16	2
Quarida	1,48125	-30,31691381	2	0,5	5	13	1
Quercy	1,399038462	-16,35804279	17,33333333	4,333333333	19,33333333	6	1
Quinder	1,433823529	-44,79579312	5	0,333333333	8,666666667	16	1
Qwara	1,362831858	-35,19178819	14,5	1,5	8	13	2
Ricky	1,512676056	-33,54672267	0,333333333	1,666666667	2,333333333	15	1
Roquette	1,768844221	-60,70658978	1	2,333333333	1,666666667	15	0,5
Uhuru	1,025423729	89,49860116	0	2	7	17	3
Wenne	0,837150127	19,603705	7,333333333	1	1,666666667	10	9

xvalda · September 22, 2021, 11:47am

Hi @cloejoly
Solution from @nirgrahamuk works like a charm. But running your code on your data, I saw a correction to make it work.

First comment though about your posting. If you post a question in the future, these are the main steps to make sure that people will be able to replicate the issue:

share the data in an easy copy/paste format, you can use the datapasta package for this (more explanations here: FAQ: How to do a minimal reproducible example ( reprex ) for beginners)
Share the code (you did it already so all good)
Open a new R session and test that the data and code you’re sharing are effectively showing the right issue

But I did this for you below and inserted my comments in your code:

Don’t rename the “value2” variable since you’re using it as argument in your plot
Replace po.nopanel by nirgrahamuk’ solution

If you run the whole block below, it should work.

If so, please flag @nirgrahamuk 's answer as the right solution.

nba <- data.frame(
  stringsAsFactors = FALSE,
  CRI = c(1.270642202,0.879781421,1.064102564,1.278431373,1.296089385,
          1.19375,1.197115385,1.054621849,1.089171975,1.159322034,
          1.278688525,1.180327869,1.358552632,1.313829787,
          1.48125,1.399038462,1.433823529,1.362831858,
          1.512676056,1.768844221,1.025423729,0.837150127),
  DS = c(13.83366893,71.49250489,14.0998227,
         39.13119004,3.242757601,-2.087402026,
         33.39066188,46.83488485,-5.118630703,
         -0.756084512,8.940206386,14.05813226,
         -10.7906219,-33.34665086,-30.31691381,
         -16.35804279,-44.79579312,-35.19178819,
         -33.54672267,-60.70658978,89.49860116,
         19.603705),
  Ascaris = c(0,3.5,0.666666667,0,9.25,0,0,0.5,0,
              0,1.5,0,0,3,2,17.33333333,5,14.5,
              0.333333333,1,0,7.333333333),
  Coccidias = c(0,3,5.666666667,2,1.5,0.5,0.666666667,
                0.5,3.5,0.5,6.5,2,0.5,1.5,0.5,
                4.333333333,0.333333333,1.5,
                1.666666667,2.333333333,2,1),
  Strongyles = c(0,7,6.333333333,10.33333333,1.75,3,
                 12.66666667,3.5,16.5,24.5,11,5,14,11,
                 5,19.33333333,8.666666667,8,
                 2.333333333,1.666666667,7,1.666666667),
  partners = c(16,16,16,15,13,5,14,14,13,16,7,8,
               7,16,13,6,16,13,15,15,17,10),
  age = c(17,17,12,11,10,10,10,9,9,10,20,4,
          2,2,1,1,1,2,1,0.5,3,9)
)


# Function to get the probability into a whole matrix not half, here is Spearman you can change it to Kendall or Pearson
cor.prob.all <- function (X, dfr = nrow(X) - 2) {
  R <- cor(X, use="pairwise.complete.obs",method="spearman")
  r2 <- R^2
  Fstat <- r2 * dfr/(1 - r2)
  R<- 1 - pf(Fstat, 1, dfr)
  R[row(R) == col(R)] <- NA
  R
}
# Change matrices to dataframes
#nba = Dataf
nbar<- as.data.frame(cor(nba[1:ncol(nba)]),method="spearman") # to a dataframe for r^2
nbap<- as.data.frame(cor.prob.all(nba[1:ncol(nba)])) # to a dataframe for p values
# Reset rownames
nbar <- data.frame(row=rownames(nbar),nbar) # create a column called "row" 
rownames(nbar) <- NULL
nbap <- data.frame(row=rownames(nbap),nbap) # create a column called "row" 
rownames(nbap) <- NULL
# Melt
library(reshape2)
nbar.m <- melt(nbar)
nbap.m <- melt(nbap)
# Classify (you can classify differently for nbar and for nbap also)         
nbar.m$value2<-cut(nbar.m$value,breaks=c(-1,-0.75,-0.5,-0.25,0,0.25,0.5,0.75,1),include.lowest=TRUE, label=c("(-0.75,-1)","(-0.5,-0.75)","(-0.25,-0.5)","(0,-0.25)","(0,0.25)","(0.25,0.5)","(0.5,0.75)","(0.75,1)")) # the label for the legend
nbap.m$value2<-cut(nbap.m$value,breaks=c(-Inf, 0.001, 0.01, 0.05),label=c("***", "** ", "*  ")) 
nbar.m<-cbind.data.frame(nbar.m,nbap.m$value,nbap.m$value2) # adding the p value and its cut to the first dataset of R coefficients

## --> [XV COMMENT]: you need to remove the two lines below, your ggplot fill argument mentions Value2, so let's keep it this way
#names(nbar.m)[4]<-paste("valuep") # change the column names of the dataframe 
#names(nbar.m)[4]<-paste("signif.")
nbar.m$row <- factor(nbar.m$row, levels=rev(unique(as.character(nbar.m$variable)))) # reorder the variable factor
# Plotting the matrix correlation heatmap
# Set options for a blank panel

## --> [XV COMMENT]: changed to nirgrahamuk's solution, works like a charm: 
po.nopanel <-list(theme(panel.background=element_blank(),panel.grid.minor=element_blank(),panel.grid.major=element_blank()))

pa<-ggplot(nbar.m, aes(row, variable)) +
  geom_tile(aes(fill=value2),colour="white") +
  scale_fill_brewer(palette = "RdYlGn",name="Correlation")+ # RColorBrewer package
  #theme(axis.text.x=theme_text(angle=-90))+
  po.nopanel
pa

cloejoly · September 24, 2021, 7:45am

Thank you so much !
Sorry about my posting, I'm a beginner on R AND on this kind of forums. I'll be more carefull !
Thanks again.

xvalda · September 24, 2021, 9:30am

no worries @cloejoly , glad you found an answer

system · October 1, 2021, 9:30am

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