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ggforest output not visible in rmarkdown #321

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grvsinghal opened this issue Jul 5, 2018 · 4 comments
Closed

ggforest output not visible in rmarkdown #321

grvsinghal opened this issue Jul 5, 2018 · 4 comments

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@grvsinghal
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Expected behavior

When I execute ggforest in R-markdown, the plot should get rendered

Actual behavior

No graph shows up

Steps to reproduce the problem

library(ggplot2)
library(survival)
library(survminer)

data("veteran")
cox = coxph(Surv(time, status) ~ karno+celltype, data = veteran)
ggforest(cox, data = veteran)

# please paste here the result of
devtools::session_info()
Session info ------------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.4.4 (2018-03-15)
 system   x86_64, mingw32             
 ui       RStudio (1.1.442)           
 language (EN)                        
 collate  English_United States.1252  
 tz       Asia/Calcutta               
 date     2018-07-05                  

Packages ----------------------------------------------------------------------------------------------------
 package    * version   date       source        
 assertthat   0.2.0     2017-04-11 CRAN (R 3.4.4)
 base       * 3.4.4     2018-03-15 local         
 bindr        0.1.1     2018-03-13 CRAN (R 3.4.4)
 bindrcpp     0.2.2     2018-03-29 CRAN (R 3.4.4)
 broom        0.4.5     2018-07-03 CRAN (R 3.4.4)
 cmprsk       2.2-7     2014-06-17 CRAN (R 3.4.4)
 colorspace   1.3-2     2016-12-14 CRAN (R 3.4.4)
 compiler     3.4.4     2018-03-15 local         
 data.table   1.11.4    2018-05-27 CRAN (R 3.4.4)
 datasets   * 3.4.4     2018-03-15 local         
 devtools     1.13.5    2018-02-18 CRAN (R 3.4.3)
 digest       0.6.15    2018-01-28 CRAN (R 3.4.3)
 dplyr        0.7.5     2018-05-19 CRAN (R 3.4.4)
 foreign      0.8-69    2017-06-22 CRAN (R 3.4.4)
 ggplot2    * 2.2.1     2016-12-30 CRAN (R 3.4.4)
 ggpubr     * 0.1.6     2017-11-14 CRAN (R 3.4.4)
 glue         1.2.0     2017-10-29 CRAN (R 3.4.4)
 graphics   * 3.4.4     2018-03-15 local         
 grDevices  * 3.4.4     2018-03-15 local         
 grid         3.4.4     2018-03-15 local         
 gridExtra    2.3       2017-09-09 CRAN (R 3.4.4)
 gtable       0.2.0     2016-02-26 CRAN (R 3.4.4)
 km.ci        0.5-2     2009-08-30 CRAN (R 3.4.4)
 KMsurv       0.1-5     2012-12-03 CRAN (R 3.4.1)
 knitr        1.20      2018-02-20 CRAN (R 3.4.4)
 labeling     0.3       2014-08-23 CRAN (R 3.4.1)
 lattice      0.20-35   2017-03-25 CRAN (R 3.4.4)
 lazyeval     0.2.1     2017-10-29 CRAN (R 3.4.4)
 magrittr   * 1.5       2014-11-22 CRAN (R 3.4.4)
 Matrix       1.2-12    2017-11-30 CRAN (R 3.4.4)
 memoise      1.1.0     2017-04-21 CRAN (R 3.4.4)
 methods    * 3.4.4     2018-03-15 local         
 mnormt       1.5-5     2016-10-15 CRAN (R 3.4.1)
 munsell      0.4.3     2016-02-13 CRAN (R 3.4.4)
 nlme         3.1-131.1 2018-02-16 CRAN (R 3.4.4)
 parallel     3.4.4     2018-03-15 local         
 pillar       1.2.3     2018-05-25 CRAN (R 3.4.4)
 pkgconfig    2.0.1     2017-03-21 CRAN (R 3.4.4)
 plyr         1.8.4     2016-06-08 CRAN (R 3.4.4)
 psych        1.8.4     2018-05-06 CRAN (R 3.4.4)
 purrr        0.2.5     2018-05-29 CRAN (R 3.4.4)
 R6           2.2.2     2017-06-17 CRAN (R 3.4.4)
 Rcpp         0.12.16   2018-03-13 CRAN (R 3.4.4)
 reshape2     1.4.3     2017-12-11 CRAN (R 3.4.4)
 rlang        0.2.1     2018-05-30 CRAN (R 3.4.4)
 scales       0.5.0     2017-08-24 CRAN (R 3.4.4)
 splines      3.4.4     2018-03-15 local         
 stats      * 3.4.4     2018-03-15 local         
 stringi      1.1.7     2018-03-12 CRAN (R 3.4.4)
 stringr      1.3.1     2018-05-10 CRAN (R 3.4.4)
 survival   * 2.41-3    2017-04-04 CRAN (R 3.4.4)
 survminer  * 0.4.2     2018-01-31 CRAN (R 3.4.4)
 survMisc     0.5.5     2018-07-05 CRAN (R 3.4.4)
 tibble       1.4.2     2018-01-22 CRAN (R 3.4.4)
 tidyr        0.8.1     2018-05-18 CRAN (R 3.4.4)
 tidyselect   0.2.4     2018-02-26 CRAN (R 3.4.4)
 tools        3.4.4     2018-03-15 local         
 utils      * 3.4.4     2018-03-15 local         
 withr        2.1.2     2018-03-15 CRAN (R 3.4.4)
 xtable       1.8-2     2016-02-05 CRAN (R 3.4.4)
 yaml         2.1.19    2018-05-01 CRAN (R 3.4.4)
 zoo          1.8-1     2018-01-08 CRAN (R 3.4.4)
@kassambara
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This issue is not reproducible on my computer.

Session info ---------------------------------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.3.2 (2016-10-31)
 system   x86_64, darwin13.4.0        
 ui       RStudio (1.1.423)           
 language (EN)                        
 collate  fr_FR.UTF-8                 
 tz       Europe/Paris                
 date     2018-07-07                  

Packages -------------------------------------------------------------------------------------------------------------------------
 package    * version    date       source                               
 assertthat   0.2.0.9000 2017-11-08 Github (hadley/assertthat@37f0a56)   
 base       * 3.3.2      2016-10-31 local                                
 bindr        0.1        2016-11-13 cran (@0.1)                          
 bindrcpp     0.2        2017-06-17 cran (@0.2)                          
 broom        0.4.3      2017-11-20 cran (@0.4.3)                        
 cmprsk       2.2-7      2014-06-17 CRAN (R 3.3.0)                       
 colorspace   1.4-0      2017-10-23 url                                  
 data.table   1.10.4     2017-02-01 cran (@1.10.4)                       
 datasets   * 3.3.2      2016-10-31 local                                
 devtools   * 1.13.1     2017-05-13 CRAN (R 3.3.2)                       
 digest       0.6.15     2018-01-28 cran (@0.6.15)                       
 dplyr        0.7.4      2017-09-28 cran (@0.7.4)                        
 foreign      0.8-67     2016-09-13 CRAN (R 3.3.2)                       
 ggplot2    * 2.2.1.9000 2018-06-30 Github (tidyverse/ggplot2@348b26f)   
 ggpubr     * 0.1.7.999  2018-06-30 local (kassambara/ggpubr@8f7fa67)    
 glue         1.2.0      2017-10-29 cran (@1.2.0)                        
 graphics   * 3.3.2      2016-10-31 local                                
 grDevices  * 3.3.2      2016-10-31 local                                
 grid         3.3.2      2016-10-31 local                                
 gridExtra    2.3        2017-09-09 cran (@2.3)                          
 gtable       0.2.0      2016-02-26 CRAN (R 3.3.0)                       
 km.ci        0.5-2      2009-08-30 CRAN (R 3.3.0)                       
 KMsurv       0.1-5      2012-12-03 CRAN (R 3.3.0)                       
 knitr        1.18       2017-12-27 cran (@1.18)                         
 labeling     0.3        2014-08-23 CRAN (R 3.3.0)                       
 lattice      0.20-34    2016-09-06 CRAN (R 3.3.2)                       
 lazyeval     0.2.1      2017-10-29 cran (@0.2.1)                        
 magrittr   * 1.5        2014-11-22 CRAN (R 3.3.0)                       
 Matrix       1.2-11     2017-08-16 CRAN (R 3.3.2)                       
 memoise      1.1.0      2017-04-21 cran (@1.1.0)                        
 methods    * 3.3.2      2016-10-31 local                                
 mnormt       1.5-5      2016-10-15 CRAN (R 3.3.0)                       
 munsell      0.4.3      2016-02-13 CRAN (R 3.3.0)                       
 nlme         3.1-131    2017-02-06 CRAN (R 3.3.2)                       
 parallel     3.3.2      2016-10-31 local                                
 pkgconfig    2.0.1      2017-03-21 cran (@2.0.1)                        
 plyr         1.8.4      2016-06-08 CRAN (R 3.3.0)                       
 psych        1.7.3.21   2017-03-22 cran (@1.7.3.2)                      
 purrr        0.2.4      2017-10-18 cran (@0.2.4)                        
 R6           2.2.2      2017-06-17 cran (@2.2.2)                        
 Rcpp         0.12.14    2017-11-23 cran (@0.12.14)                      
 reshape2     1.4.3      2017-12-11 cran (@1.4.3)                        
 rlang        0.2.0.9001 2018-06-30 Github (tidyverse/rlang@ba4fb06)     
 scales       0.5.0.9000 2018-06-17 Github (hadley/scales@4056ec3)       
 splines      3.3.2      2016-10-31 local                                
 stats      * 3.3.2      2016-10-31 local                                
 stringi      1.1.6      2017-11-17 cran (@1.1.6)                        
 stringr      1.3.0      2018-02-19 cran (@1.3.0)                        
 survival   * 2.41-3     2017-04-04 CRAN (R 3.3.2)                       
 survminer  * 0.3.1.999  2017-06-05 Github (kassambara/survminer@8511dee)
 survMisc     0.5.4      2016-11-23 CRAN (R 3.3.2)                       
 tibble       1.3.4      2017-08-22 cran (@1.3.4)                        
 tidyr        0.8.1.9000 2018-06-30 Github (tidyverse/tidyr@cbdd14e)     
 tools        3.3.2      2016-10-31 local                                
 utils      * 3.3.2      2016-10-31 local                                
 withr        2.1.2      2018-06-30 Github (jimhester/withr@fe56f20)     
 xtable       1.8-2      2016-02-05 CRAN (R 3.3.0)                       
 yaml         2.1.16     2017-12-12 cran (@2.1.16)                       
 zoo          1.7-14     2016-12-16 CRAN (R 3.3.2)

@grvsinghal
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Thanks for quick response, I earlier asked a resolution of this issue on stack overflow (here). I have asked the person who replied, to confirm whether he was able to reproduce the issue.

kassambara added a commit that referenced this issue Jul 9, 2018
@kassambara
now ggforest returns a ggplot instead of drawing #321
95ba381
@kassambara
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Owner

I made a minor change in ggforest function. Does it fix this issue?

@grvsinghal
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grvsinghal commented Jul 10, 2018 •
edited
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Thanks, now it shows the output, however, before actual graph, it creates an empty chart.
I have got a workaround by assigning a name to the plot and then calling that name in next chunk. Issue of blank chart or non-plotting or double-plotting never occurred when I plot it in the next chunk.

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@kassambara @grvsinghal