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20 hours ago •
kassambara
kassambara
Error R2 with stat_cor function
I tried to use the stat_cor, stat_regline_equation and stat_smooth function to perform statistics on a scatter plot, and I wanted to try both the y~log(x,base=2) and y~x formula simultaneously. However, the final results showed that the R2 and P values obtained from both functions were same. Even when I commented out one group of the stat_smooth, stat_cor, and stat_regline_equation functions, the results remained the same. Is this right or Bug?
Expected behavior
Draw stat_cor with formula y= log(x,base=2) and y=x in same plot , Show different R2 value
Actual behavior
Draw stat_cor with formula y~log(x,base=2) and y~x in same plot , Show same R2 value
Steps to reproduce the problem
Draw stat_cor with formula y~ log(x,base=2) and y~x in same plot
draw_mean_pic<-function(tmp_data){
ssp_data_means<- ggscatter(tmp_data,x="Original",y="Normalized")+
# try draw with formula =y~x
stat_smooth(method='lm', se=FALSE, color='turquoise4' ,formula =y~x) +
stat_cor(aes( label =paste(..rr.label.., ..p.label.., sep = "~`,`~")),check_overlap = TRUE,label.y.npc=0.9,label.x.npc=0.02) +
stat_regline_equation( check_overlap = TRUE,label.y.npc=0.98,label.x.npc=0.02 ,formula =y~x)+
xlab("Original Mean") +
ylab("Normalized Mean") +
stat_smooth(method = "lm", se=T,formula =y ~ log(x,base = 2) )+
stat_cor(aes( label =paste(..rr.label.., ..p.label.., sep = "~`,`~")),check_overlap = TRUE,label.y.npc=0.76,label.x.npc=0.02)+
stat_regline_equation(
check_overlap = TRUE,
aes(label = sub("x", "log2(x)", ..eq.label..)),
formula = y ~ log(x,base = 2),
label.y.npc=0.84,label.x.npc=0.02
)+
ggtitle("Comparison of Mean before and after Normalization")
ssp_data_means
}
draw_mean_pic(data)
session_info()
setting value
version R version 4.3.1 (2023-06-16)
os UnionTech OS Desktop 20 Home
system x86_64, linux-gnu
ui RStudio
language zh_CN
collate C.UTF-8
ctype C.UTF-8
tz Asia/Beijing
date 2024-03-29
rstudio 1.1.456 (desktop)
pandoc 2.12 @ /home/liuxiawei/micromamba/envs/r/bin/ (via rmarkdown)
─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 4.3.1)
ape 5.7-1 2023-03-13 [1] CRAN (R 4.3.1)
backports 1.4.1 2021-12-13 [1] CRAN (R 4.3.1)
beeswarm 0.4.0 2021-06-01 [1] CRAN (R 4.3.1)
biglm 0.9-2.1 2020-11-27 [1] CRAN (R 4.3.1)
Biobase 2.62.0 2023-10-24 [1] Bioconductor
BiocGenerics * 0.48.1 2023-11-01 [1] Bioconductor
BiocParallel * 1.36.0 2023-10-24 [1] Bioconductor
bit 4.0.5 2022-11-15 [1] CRAN (R 4.3.1)
bit64 4.0.5 2020-08-30 [1] CRAN (R 4.3.1)
bitops 1.0-7 2021-04-24 [1] CRAN (R 4.3.1)
broom 1.0.5 2023-06-09 [1] CRAN (R 4.3.1)
bslib 0.6.1 2023-11-28 [1] CRAN (R 4.3.1)
cachem 1.0.8 2023-05-01 [1] CRAN (R 4.3.1)
car 3.1-2 2023-03-30 [1] CRAN (R 4.3.1)
carData 3.0-5 2022-01-06 [1] CRAN (R 4.3.1)
Cardinal 3.4.3 2023-11-23 [1] Bioconductor 3.18 (R 4.3.1)
CardinalIO 1.0.0 2023-10-24 [1] Bioconductor
cli 3.6.2 2023-12-11 [1] CRAN (R 4.3.2)
cluster 2.1.6 2023-12-01 [1] CRAN (R 4.3.1)
codetools 0.2-19 2023-02-01 [1] CRAN (R 4.3.1)
colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.3.1)
confintr 1.0.2 2023-06-04 [1] CRAN (R 4.3.1)
cowplot 1.1.3 2024-01-22 [1] CRAN (R 4.3.1)
crayon 1.5.2 2022-09-29 [1] CRAN (R 4.3.1)
data.table 1.15.2 2024-02-29 [1] CRAN (R 4.3.1)
DBI 1.2.2 2024-02-16 [1] CRAN (R 4.3.2)
DelayedArray 0.28.0 2023-10-24 [1] Bioconductor
DelayedMatrixStats 1.24.0 2023-10-24 [1] Bioconductor
deldir 2.0-4 2024-02-28 [1] CRAN (R 4.3.1)
devtools 2.4.5 2022-10-11 [1] CRAN (R 4.3.1)
digest 0.6.35 2024-03-11 [1] CRAN (R 4.3.1)
dotCall64 1.1-1 2023-11-28 [1] CRAN (R 4.3.1)
dplyr * 1.1.4 2023-11-17 [1] CRAN (R 4.3.2)
EBImage * 4.44.0 2023-10-24 [1] Bioconductor
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.3.1)
evaluate 0.23 2023-11-01 [1] CRAN (R 4.3.1)
fansi 1.0.6 2023-12-08 [1] CRAN (R 4.3.1)
farver 2.1.1 2022-07-06 [1] CRAN (R 4.3.1)
fastDummies 1.7.3 2023-07-06 [1] CRAN (R 4.3.1)
fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.1)
fftwtools 0.9-11 2021-03-01 [1] CRAN (R 4.3.1)
fitdistrplus 1.1-11 2023-04-25 [1] CRAN (R 4.3.1)
fs 1.6.3 2023-07-20 [1] CRAN (R 4.3.1)
future 1.33.1 2023-12-22 [1] CRAN (R 4.3.2)
future.apply 1.11.1 2023-12-21 [1] CRAN (R 4.3.2)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.1)
GenomeInfoDb 1.38.8 2024-03-15 [1] Bioconductor 3.18 (R 4.3.1)
GenomeInfoDbData 1.2.11 2024-03-20 [1] Bioconductor
GenomicRanges 1.54.1 2023-10-29 [1] Bioconductor
ggbeeswarm 0.7.2 2023-04-29 [1] CRAN (R 4.3.1)
ggplot2 * 3.5.0 2024-02-23 [1] CRAN (R 4.3.1)
ggpmisc * 0.5.5 2023-11-15 [1] CRAN (R 4.3.1)
ggpp * 0.5.6 2024-01-09 [1] CRAN (R 4.3.1)
ggpubr * 0.6.0 2023-02-10 [1] CRAN (R 4.3.1)
ggrastr 1.0.2 2023-06-01 [1] CRAN (R 4.3.1)
ggrepel 0.9.5 2024-01-10 [1] CRAN (R 4.3.1)
ggridges 0.5.6 2024-01-23 [1] CRAN (R 4.3.1)
ggsignif 0.6.4 2022-10-13 [1] CRAN (R 4.3.1)
glmGamPoi 1.14.3 2024-02-11 [1] Bioconductor 3.18 (R 4.3.1)
globals 0.16.3 2024-03-08 [1] CRAN (R 4.3.3)
glue 1.7.0 2024-01-09 [1] CRAN (R 4.3.1)
goftest 1.2-3 2021-10-07 [1] CRAN (R 4.3.1)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.3.1)
gtable 0.3.4 2023-08-21 [1] CRAN (R 4.3.1)
hdf5r 1.3.10 2024-03-02 [1] CRAN (R 4.3.1)
htmltools 0.5.7 2023-11-03 [1] CRAN (R 4.3.1)
htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.3.1)
httpuv 1.6.14 2024-01-26 [1] CRAN (R 4.3.1)
httr 1.4.7 2023-08-15 [1] CRAN (R 4.3.1)
ica 1.0-3 2022-07-08 [1] CRAN (R 4.3.1)
igraph 2.0.3 2024-03-13 [1] CRAN (R 4.3.1)
IRanges 2.36.0 2023-10-24 [1] Bioconductor
irlba 2.3.5.1 2022-10-03 [1] CRAN (R 4.3.1)
jpeg 0.1-10 2022-11-29 [1] CRAN (R 4.3.1)
jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.3.1)
jsonlite 1.8.8 2023-12-04 [1] CRAN (R 4.3.1)
KernSmooth 2.23-22 2023-07-10 [1] CRAN (R 4.3.1)
knitr 1.45 2023-10-30 [1] CRAN (R 4.3.1)
labeling 0.4.3 2023-08-29 [1] CRAN (R 4.3.1)
later 1.3.2 2023-12-06 [1] CRAN (R 4.3.1)
lattice 0.22-6 2024-03-20 [1] CRAN (R 4.3.1)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.3.1)
leiden 0.4.3.1 2023-11-17 [1] CRAN (R 4.3.1)
lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.3.2)
listenv 0.9.1 2024-01-29 [1] CRAN (R 4.3.1)
lmodel2 1.7-3 2018-02-05 [1] CRAN (R 4.3.1)
lmtest 0.9-40 2022-03-21 [1] CRAN (R 4.3.1)
locfit 1.5-9.9 2024-03-01 [1] CRAN (R 4.3.1)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.1)
MASS 7.3-60.0.1 2024-01-13 [1] CRAN (R 4.3.1)
Matrix 1.6-5 2024-01-11 [1] CRAN (R 4.3.1)
MatrixGenerics 1.14.0 2023-10-24 [1] Bioconductor
MatrixModels 0.5-3 2023-11-06 [1] CRAN (R 4.3.1)
matrixStats 1.2.0 2023-12-11 [1] CRAN (R 4.3.1)
matter 2.4.1 2024-03-13 [1] Bioconductor 3.18 (R 4.3.1)
mclust 6.1 2024-02-23 [1] CRAN (R 4.3.1)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.1)
mgcv 1.9-1 2023-12-21 [1] CRAN (R 4.3.1)
mime 0.12 2021-09-28 [1] CRAN (R 4.3.1)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.3.1)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.3.1)
nlme 3.1-164 2023-11-27 [1] CRAN (R 4.3.1)
ontologyIndex 2.12 2024-02-27 [1] CRAN (R 4.3.1)
parallelly 1.37.1 2024-02-29 [1] CRAN (R 4.3.1)
patchwork * 1.2.0 2024-01-08 [1] CRAN (R 4.3.1)
pbapply 1.7-2 2023-06-27 [1] CRAN (R 4.3.1)
pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.1)
pkgbuild 1.4.4 2024-03-17 [1] CRAN (R 4.3.1)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.1)
pkgload 1.3.4 2024-01-16 [1] CRAN (R 4.3.1)
plotly 4.10.4 2024-01-13 [1] CRAN (R 4.3.1)
plyr 1.8.9 2023-10-02 [1] CRAN (R 4.3.1)
png 0.1-8 2022-11-29 [1] CRAN (R 4.3.1)
polyclip 1.10-6 2023-09-27 [1] CRAN (R 4.3.1)
polynom 1.4-1 2022-04-11 [1] CRAN (R 4.3.1)
profvis 0.3.8 2023-05-02 [1] CRAN (R 4.3.1)
progressr 0.14.0 2023-08-10 [1] CRAN (R 4.3.1)
promises 1.2.1 2023-08-10 [1] CRAN (R 4.3.1)
ProtGenerics * 1.34.0 2023-10-24 [1] Bioconductor
purrr 1.0.2 2023-08-10 [1] CRAN (R 4.3.1)
quantreg 5.97 2023-08-19 [1] CRAN (R 4.3.1)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.1)
RANN 2.6.1 2019-01-08 [1] CRAN (R 4.3.1)
RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.3.1)
Rcpp 1.0.12 2024-01-09 [1] CRAN (R 4.3.1)
RcppAnnoy 0.0.22 2024-01-23 [1] CRAN (R 4.3.1)
RcppHNSW 0.6.0 2024-02-04 [1] CRAN (R 4.3.1)
RCurl 1.98-1.14 2024-01-09 [1] CRAN (R 4.3.1)
remotes 2.5.0 2024-03-17 [1] CRAN (R 4.3.1)
reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.3.1)
reticulate 1.35.0 2024-01-31 [1] CRAN (R 4.3.1)
rlang 1.1.3 2024-01-10 [1] CRAN (R 4.3.1)
rmarkdown 2.26 2024-03-05 [1] CRAN (R 4.3.1)
ROCR 1.0-11 2020-05-02 [1] CRAN (R 4.3.1)
RSpectra 0.16-1 2022-04-24 [1] CRAN (R 4.3.1)
rstatix 0.7.2 2023-02-01 [1] CRAN (R 4.3.1)
rstudioapi 0.15.0 2023-07-07 [1] CRAN (R 4.3.1)
Rtsne 0.17 2023-12-07 [1] CRAN (R 4.3.1)
S4Arrays 1.2.1 2024-03-04 [1] Bioconductor 3.18 (R 4.3.1)
S4Vectors * 0.40.2 2023-11-23 [1] Bioconductor 3.18 (R 4.3.2)
sass 0.4.9 2024-03-15 [1] CRAN (R 4.3.1)
scales * 1.3.0 2023-11-28 [1] CRAN (R 4.3.1)
scattermore 1.2 2023-06-12 [1] CRAN (R 4.3.1)
sctransform 0.4.1 2023-10-19 [1] CRAN (R 4.3.1)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.1)
Seurat * 5.0.3 2024-03-18 [1] CRAN (R 4.3.1)
SeuratDisk * 0.0.0.9021 2024-03-18 [1] Github (mojaveazure/seurat-disk@877d4e1)
SeuratObject * 5.0.1 2023-11-17 [1] CRAN (R 4.3.2)
shiny 1.8.0 2023-11-17 [1] CRAN (R 4.3.1)
signal 1.8-0 2023-11-27 [1] CRAN (R 4.3.1)
sp * 2.1-3 2024-01-30 [1] CRAN (R 4.3.2)
spam 2.10-0 2023-10-23 [1] CRAN (R 4.3.1)
SparseArray 1.2.4 2024-02-11 [1] Bioconductor 3.18 (R 4.3.1)
SparseM 1.81 2021-02-18 [1] CRAN (R 4.3.1)
sparseMatrixStats 1.14.0 2023-10-24 [1] Bioconductor
spatstat.data 3.0-4 2024-01-15 [1] CRAN (R 4.3.2)
spatstat.explore 3.2-6 2024-02-01 [1] CRAN (R 4.3.2)
spatstat.geom 3.2-9 2024-02-28 [1] CRAN (R 4.3.2)
spatstat.random 3.2-3 2024-02-29 [1] CRAN (R 4.3.3)
spatstat.sparse 3.0-3 2023-10-24 [1] CRAN (R 4.3.1)
spatstat.utils 3.0-4 2023-10-24 [1] CRAN (R 4.3.1)
stringi 1.8.3 2023-12-11 [1] CRAN (R 4.3.1)
stringr 1.5.1 2023-11-14 [1] CRAN (R 4.3.2)
SummarizedExperiment 1.32.0 2023-10-24 [1] Bioconductor
survival 3.5-8 2024-02-14 [1] CRAN (R 4.3.1)
tensor 1.5 2012-05-05 [1] CRAN (R 4.3.1)
tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.1)
tidyr 1.3.1 2024-01-24 [1] CRAN (R 4.3.2)
tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.3.1)
tiff 0.1-12 2023-11-28 [1] CRAN (R 4.3.1)
urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.3.1)
usethis 2.2.3 2024-02-19 [1] CRAN (R 4.3.1)
utf8 1.2.4 2023-10-22 [1] CRAN (R 4.3.1)
uwot 0.1.16 2023-06-29 [1] CRAN (R 4.3.1)
vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.3.2)
vipor 0.4.7 2023-12-18 [1] CRAN (R 4.3.1)
viridisLite 0.4.2 2023-05-02 [1] CRAN (R 4.3.1)
withr 3.0.0 2024-01-16 [1] CRAN (R 4.3.1)
xfun 0.42 2024-02-08 [1] CRAN (R 4.3.1)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.3.1)
XVector 0.42.0 2023-10-24 [1] Bioconductor
yaml 2.3.8 2023-12-11 [1] CRAN (R 4.3.1)
zlibbioc 1.48.2 2024-03-13 [1] Bioconductor 3.18 (R 4.3.1)
zoo 1.8-12 2023-04-13 [1] CRAN (R 4.3.1)
