I am preparing a pull request for velociraptor (https://github.com/kevinrue/velociraptor/pull/30) that would use metR to visualize RNA velocities estimated from single cell transcriptomics data in reduced dimensional space.
I have run into a problem when using metR::geom_streamline if ggplot2 is only attached via it's namespace. The problem can be reproduced using the following code:
df <- data.frame(expand.grid(x = 1:10, y = 1:10), dx = rnorm(100), dy = rnorm(100))
ggplot2::ggplot(df, ggplot2::aes(x,y)) + ggplot2::geom_point() + metR::geom_streamline(ggplot2::aes(dx = dx, dy = dy))
In a fresh R session without any loaded packages, this throws: Error in coord_munch(coord, data, panel_params) : could not find function "coord_munch". After library(ggplot2) however, things work fine.
Would you consider adding the namespace to such calls, e.g. changing the above line to:
munched <- ggplot2::coord_munch(coord, data, panel_params)
in order to make metR::geom_streamline usable also with non-attached ggplot2?
I am using:
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /tungstenfs/groups/gbioinfo/Appz/easybuild/software/OpenBLAS/0.3.7-GCC-8.3.0/lib/libopenblas_skylakex-r0.3.7.so
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RColorBrewer_1.1-2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 magrittr_2.0.1 maps_3.3.0 tidyselect_1.1.0 munsell_0.5.0 colorspace_2.0-0 R6_2.5.0
[8] rlang_0.4.9 dplyr_1.0.2 fields_11.6 dotCall64_1.0-0 grid_4.0.3 spam_2.6-0 checkmate_2.0.0
[15] data.table_1.13.4 gtable_0.3.0 metR_0.9.0 ellipsis_0.3.1 fortunes_1.5-4 digest_0.6.27 tibble_3.0.4
[22] lifecycle_0.2.0 crayon_1.3.4 farver_2.0.3 purrr_0.3.4 ggplot2_3.3.2 vctrs_0.3.6 memoise_1.1.0
[29] glue_1.4.2 labeling_0.4.2 compiler_4.0.3 pillar_1.4.7 generics_0.1.0 scales_1.1.1 backports_1.2.1
[36] lubridate_1.7.9.2 pkgconfig_2.0.3
Thank you for the great
metR
package!I am preparing a pull request for
velociraptor
(https://github.com/kevinrue/velociraptor/pull/30) that would usemetR
to visualize RNA velocities estimated from single cell transcriptomics data in reduced dimensional space.I have run into a problem when using
metR::geom_streamline
ifggplot2
is only attached via it's namespace. The problem can be reproduced using the following code:In a fresh R session without any loaded packages, this throws:
Error in coord_munch(coord, data, panel_params) : could not find function "coord_munch"
. Afterlibrary(ggplot2)
however, things work fine.My guess is that this is caused by: https://github.com/eliocamp/metR/blob/012bcffaab45899c6ec08badef0e23e4ca93b7d2/R/geom_streamline.R#L298
Would you consider adding the namespace to such calls, e.g. changing the above line to:
munched <- ggplot2::coord_munch(coord, data, panel_params)
in order to makemetR::geom_streamline
usable also with non-attachedggplot2
?I am using: