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thomasp85
negative values for plot margins theme not respected?
Hi,
I'm encountering an issue when combining plots with the latest version of patchwork. This was raised in my repo zktuong/ktplots#7 and I found that this was previously working with patchwork_0.0.1 but not in patchwork_1.0.1.
I think the problem is that negative values in theme(plot.margin = unit(c(-0.75, 0, -0.75, 0), "cm")) were not respected somehow? Doesn't seem to a problem with ggplot2 itself and simply downgrading to patchwork_0.0.1 solved it.
Any advice going forward will be greatly appreciated.
The full code of the function(s) is here:
#' Plotting stacked violin plot
#'
## main function
#' @name StackedVlnPlot
#' @param obj single-cell data. can be seurat/summarizedexperiment object
#' @param features genes/features to plot
#' @param pt.size size of dots
#' @param plot.margin to adjust the white space between each plot.
#' @param ... passed to Seurat::VlnPlot
#' @return StackedVlnPlot
#' @source \url{https://divingintogeneticsandgenomics.rbind.io/post/stacked-violin-plot-for-visualizing-single-cell-data-in-seurat/}
#' @examples
#' data(kidneyimmune)
#' features<- c("CD79A", "MS4A1", "CD8A", "CD8B", "LYZ", "LGALS3", "S100A8", "GNLY", "NKG7", "KLRB1", "FCGR3A", "FCER1A", "CST3")
#' StackedVlnPlot(kidneyimmune, features = features) + theme(axis.text.x = element_text(angle = 90, hjust = 1, size = 8))
#' @import ggplot2
#' @import purrr
#' @import patchwork
#' @export
StackedVlnPlot <- function(obj, features,
pt.size = 0,
plot.margin = unit(c(-0.75, 0, -0.75, 0), "cm"),
...) {
requireNamespace('purrr')
plot_list<- purrr::map(features, function(x) modify_vlnplot(obj = obj,feature = x, ...))
# Add back x-axis title to bottom plot. patchwork is going to support this?
plot_list[[length(plot_list)]]<- plot_list[[length(plot_list)]] +
theme(axis.text.x=element_text(), axis.ticks.x = element_line())
# change the y-axis tick to only max value
ymaxs<- purrr::map_dbl(plot_list, extract_max)
plot_list<- purrr::map2(plot_list, ymaxs, function(x,y) x +
scale_y_continuous(breaks = c(y)) +
expand_limits(y = y))
requireNamespace('patchwork')
p <- patchwork::wrap_plots(plotlist = plot_list, ncol = 1) ##### this is where i think it's going wrong
return(p)
}
## remove the x-axis text and tick
#' @name misc
#' @param obj single-cell data. can be seurat/summarizedexperiment object
#' @param feature genes/features to plot
#' @param pt.size size of dots
#' @param plot.margin to adjust the white space between each plot.
#' @param ... passed to Seurat::VlnPlot
#' @export
modify_vlnplot<- function(obj,
feature,
pt.size = 0,
plot.margin = unit(c(-0.75, 0, -0.75, 0), "cm"),
...) {
p<- Seurat::VlnPlot(obj, features = feature, pt.size = pt.size, ... ) +
xlab("") + ylab(feature) + ggtitle("") +
theme(legend.position = "none",
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
axis.title.y = element_text(size = rel(1), angle = 0),
axis.text.y = element_text(size = rel(1)),
plot.margin = plot.margin )
return(p)
}
## extract the max value of the y axis
#' @name misc
#' @param p value
#' @export
extract_max<- function(p){
ymax<- max(ggplot_build(p)$layout$panel_scales_y[[1]]$range$range)
return(ceiling(ymax))
}
> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.15.5
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] patchwork_0.0.1 ktplots_1.1.6 ggplot2_3.2.1
loaded via a namespace (and not attached):
[1] tsne_0.1-3 nlme_3.1-141 bitops_1.0-6 fs_1.3.1 usethis_1.5.1
[6] devtools_2.2.2 RcppAnnoy_0.0.14 RColorBrewer_1.1-2 httr_1.4.1 rprojroot_1.3-2
[11] sctransform_0.2.0 tools_3.6.0 backports_1.1.5 R6_2.4.1 irlba_2.3.3
[16] KernSmooth_2.23-15 uwot_0.1.4 lazyeval_0.2.2 colorspace_1.4-1 npsurv_0.4-0
[21] withr_2.1.2 tidyselect_1.0.0 gridExtra_2.3 prettyunits_1.1.1 processx_3.4.2
[26] compiler_3.6.0 cli_2.0.1 plotly_4.9.1 desc_1.2.0 labeling_0.3
[31] Seurat_3.1.1 caTools_1.17.1.2 scales_1.1.0 lmtest_0.9-37 pbapply_1.4-2
[36] ggridges_0.5.1 callr_3.4.2 stringr_1.4.0 digest_0.6.25 R.utils_2.9.0
[41] htmltools_0.4.0 pkgconfig_2.0.3 bibtex_0.4.2 sessioninfo_1.1.1 htmlwidgets_1.5.1
[46] rlang_0.4.4 farver_2.0.3 zoo_1.8-6 jsonlite_1.6.1 ica_1.0-2
[51] gtools_3.8.1 dplyr_0.8.4 R.oo_1.23.0 magrittr_1.5 Matrix_1.2-17
[56] Rcpp_1.0.3 munsell_0.5.0 fansi_0.4.1 reticulate_1.13 ape_5.3
[61] viridis_0.5.1 lifecycle_0.1.0 R.methodsS3_1.7.1 stringi_1.4.6 gbRd_0.4-11
[66] MASS_7.3-51.4 pkgbuild_1.0.6 gplots_3.0.1.1 Rtsne_0.15 plyr_1.8.5
[71] grid_3.6.0 parallel_3.6.0 gdata_2.18.0 listenv_0.7.0 ggrepel_0.8.1
[76] crayon_1.3.4 lattice_0.20-38 cowplot_1.0.0 splines_3.6.0 SDMTools_1.1-221.1
[81] ps_1.3.2 pillar_1.4.3 igraph_1.2.4.1 future.apply_1.3.0 reshape2_1.4.3
[86] codetools_0.2-16 pkgload_1.0.2 leiden_0.3.1 glue_1.3.1 lsei_1.2-0
[91] metap_1.1 RcppParallel_4.4.4 data.table_1.12.6 remotes_2.1.1 png_0.1-7
[96] vctrs_0.2.3 Rdpack_0.11-0 testthat_2.3.1 tidyr_1.0.0 gtable_0.3.0
[101] RANN_2.6.1 purrr_0.3.3 future_1.15.0 assertthat_0.2.1 rsvd_1.0.2
[106] survival_2.44-1.1 viridisLite_0.3.0 tibble_2.1.3 memoise_1.1.0 cluster_2.1.0
[111] globals_0.12.4 fitdistrplus_1.0-14 ellipsis_0.3.0 ROCR_1.0-7
A recent bug-fix removed the possibility of having negative margins. I'm pretty sure that negative widths and heights of any kind is not really supported in grid (which resulted in the bug that started all this).
If it makes a difference, I often find that using negative plot margins is useful for organizing patches. If it is possible to support this feature, I would greatly appreciate it.
I agree with jhrcook - I would also highly appreciate the possibility of negative margins!
