No visible plots for interactive CARP plots
Opened this issue · 6 comments
I tried to play with a carp fit on the first 100 points from the data in #54, but the Shiny app wasn't displaying any graphics, just the regularization slider.
I also gave up on type = "dynamic_path" after 2 or so minutes of rendering.
Will check out the lack of graphics issue tomorrow. Possibly a slowness issue, but my default test data has n = 44 so I can't imagine there being too big a difference.
(I have long term goal of removing shiny and doing it all in D3, but I'm not knowledgeable enough about D3 to do it right now)
Re: type = "dynamic_path" -- can you send session info? (Either the devtools version or the base R one) I've seen that hang when the wrong version of gganimate was being invoked and/or gifski was not installed properly, but want to confirm.
devtools::session_info()
Session info --------------------------------------------------------------------------
setting value
version R version 3.5.0 (2018-04-23)
system x86_64, mingw32
ui RStudio (1.2.999)
language (EN)
collate English_United States.1252
tz America/Chicago
date 2018-10-11
Packages ------------------------------------------------------------------------------
package * version date source
animation 2.5 2017-03-30 CRAN (R 3.5.1)
assertthat 0.2.0 2017-04-11 CRAN (R 3.5.0)
backports 1.1.2 2017-12-13 CRAN (R 3.5.0)
base * 3.5.0 2018-04-23 local
bindr 0.1.1 2018-03-13 CRAN (R 3.5.0)
bindrcpp 0.2.2 2018-03-29 CRAN (R 3.5.0)
class 7.3-14 2015-08-30 CRAN (R 3.5.0)
cluster 2.0.7-1 2018-04-13 CRAN (R 3.5.0)
clustRviz * 0.1.0 2018-10-07 Github (DataSlingers/clustRviz@39dc90a)
colorspace 1.3-2 2016-12-14 CRAN (R 3.5.0)
compiler 3.5.0 2018-04-23 local
crayon 1.3.4 2017-09-16 CRAN (R 3.5.0)
datasets * 3.5.0 2018-04-23 local
dendextend 1.8.0 2018-05-03 CRAN (R 3.5.0)
DEoptimR 1.0-8 2016-11-19 CRAN (R 3.5.0)
devtools 1.13.6 2018-06-27 CRAN (R 3.5.0)
digest 0.6.17 2018-09-12 CRAN (R 3.5.1)
diptest 0.75-7 2016-12-05 CRAN (R 3.5.0)
dplyr 0.7.6 2018-06-29 CRAN (R 3.5.1)
evaluate 0.11 2018-07-17 CRAN (R 3.5.1)
farver 1.0.0.9999 2018-09-27 Github (thomasp85/farver@5439336)
flexmix 2.3-14 2017-04-28 CRAN (R 3.5.0)
fpc 2.1-11.1 2018-07-20 CRAN (R 3.5.1)
gganimate 0.9.9.9999 2018-09-27 Github (thomasp85/gganimate@b1dce00)
ggplot2 3.0.0 2018-07-03 CRAN (R 3.5.1)
ggrepel 0.8.0 2018-05-09 CRAN (R 3.5.1)
gifski 0.8.3 2018-07-20 CRAN (R 3.5.1)
glue 1.3.0 2018-08-26 Github (tidyverse/glue@4e74901)
graphics * 3.5.0 2018-04-23 local
grDevices * 3.5.0 2018-04-23 local
grid 3.5.0 2018-04-23 local
gridExtra 2.3 2017-09-09 CRAN (R 3.5.0)
gtable 0.2.0 2016-02-26 CRAN (R 3.5.0)
gtools 3.8.1 2018-06-26 CRAN (R 3.5.0)
hms 0.4.2 2018-03-10 CRAN (R 3.5.0)
htmltools 0.3.6 2017-04-28 CRAN (R 3.5.0)
httpuv 1.4.5 2018-07-19 CRAN (R 3.5.1)
kernlab 0.9-27 2018-08-10 CRAN (R 3.5.1)
knitr 1.20 2018-02-20 CRAN (R 3.5.0)
later 0.7.5 2018-09-18 CRAN (R 3.5.1)
lattice 0.20-35 2017-03-25 CRAN (R 3.5.0)
lazyeval 0.2.1 2017-10-29 CRAN (R 3.5.0)
magrittr 1.5 2014-11-22 CRAN (R 3.5.0)
MASS 7.3-49 2018-02-23 CRAN (R 3.5.0)
Matrix 1.2-14 2018-04-13 CRAN (R 3.5.0)
mclust 5.4.1 2018-06-27 CRAN (R 3.5.0)
memoise 1.1.0 2017-04-21 CRAN (R 3.5.0)
methods * 3.5.0 2018-04-23 local
mime 0.5 2016-07-07 CRAN (R 3.5.0)
modeltools 0.2-22 2018-07-16 CRAN (R 3.5.1)
munsell 0.5.0 2018-06-12 CRAN (R 3.5.0)
mvtnorm 1.0-8 2018-05-31 CRAN (R 3.5.0)
nnet 7.3-12 2016-02-02 CRAN (R 3.5.0)
packrat 0.4.9-3 2018-06-01 CRAN (R 3.5.0)
pillar 1.3.0 2018-07-14 CRAN (R 3.5.1)
pkgconfig 2.0.2 2018-08-16 CRAN (R 3.5.1)
plyr 1.8.4 2016-06-08 CRAN (R 3.5.0)
png 0.1-7 2013-12-03 CRAN (R 3.5.0)
prabclus 2.2-6 2015-01-14 CRAN (R 3.5.0)
prettyunits 1.0.2 2015-07-13 CRAN (R 3.5.0)
progress 1.2.0 2018-06-27 Github (r-lib/progress@8428528)
promises 1.0.1 2018-04-13 CRAN (R 3.5.0)
purrr 0.2.5 2018-05-29 CRAN (R 3.5.0)
R6 2.2.2 2017-06-17 CRAN (R 3.5.0)
RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.5.0)
Rcpp 0.12.19.1 2018-10-01 Github (RcppCore/Rcpp@4680c31)
rlang 0.2.2.9001 2018-10-01 Github (r-lib/rlang@cdb713c)
rmarkdown 1.10 2018-06-11 CRAN (R 3.5.0)
robustbase 0.93-3 2018-09-21 CRAN (R 3.5.1)
rprojroot 1.3-2 2018-01-03 CRAN (R 3.5.0)
rstudioapi 0.7 2017-09-07 CRAN (R 3.5.0)
scales 1.0.0 2018-08-09 CRAN (R 3.5.1)
shiny 1.1.0 2018-05-17 CRAN (R 3.5.0)
stats * 3.5.0 2018-04-23 local
stats4 3.5.0 2018-04-23 local
stringi 1.1.7 2018-03-12 CRAN (R 3.5.0)
stringr 1.3.1 2018-05-10 CRAN (R 3.5.0)
tibble 1.4.2 2018-01-22 CRAN (R 3.5.0)
tidyr 0.8.1 2018-05-18 CRAN (R 3.5.0)
tidyselect 0.2.4 2018-02-26 CRAN (R 3.5.0)
tools 3.5.0 2018-04-23 local
trimcluster 0.1-2.1 2018-07-20 CRAN (R 3.5.1)
tweenr 0.1.5.9999 2018-09-27 Github (thomasp85/tweenr@48ea2fd)
utils * 3.5.0 2018-04-23 local
viridis 0.5.1 2018-03-29 CRAN (R 3.5.0)
viridisLite 0.3.0 2018-02-01 CRAN (R 3.5.0)
whisker 0.3-2 2013-04-28 CRAN (R 3.5.0)
withr 2.1.2 2018-03-15 CRAN (R 3.5.0)
xtable 1.8-3 2018-08-29 CRAN (R 3.5.1)
zoo 1.8-4 2018-09-19 CRAN (R 3.5.1) I also tried some static plots for the scaled data and there was a ton of overplotting. I imagine the absolute number of points in the paths grows with the number of data points and this slows things down a lot? Maybe there's some heuristic to no use all the points on the paths / not label things when there are 2000 points that will speed stuff up as well.
So I've looked into this and there's definitely some room for improvement -- we plot the centroid for each point at each iteration, which (as you note) leads to overplotting for fused centroids. Once "U smoothing" (#63) is added to the post-processing, we can add a distinct() filter before plotting which should speed things up majorly.
That said, I think there are always going to be some problems with larger data sets + shiny graphics since ggplot2 (or really grid) is slow (vs base graphics). I've got some long term ideas about moving away from ggplot2 but they aren't likely to happen for a while.
RStudio also just hired someone to make ggplot2 faster, which with any luck will result in noticeable speed improvements across the board.