From aef4c98b6d9875bbbc440cecba8cb8f1889b8de1 Mon Sep 17 00:00:00 2001 From: naikymen Date: Tue, 29 Oct 2024 18:20:54 -0300 Subject: [PATCH] templates: minor improvements to quick guide --- .../rmd_template.cellid_quick/skeleton/skeleton.Rmd | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/inst/rmarkdown/templates/rmd_template.cellid_quick/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/rmd_template.cellid_quick/skeleton/skeleton.Rmd index a46c09c..aba054a 100644 --- a/inst/rmarkdown/templates/rmd_template.cellid_quick/skeleton/skeleton.Rmd +++ b/inst/rmarkdown/templates/rmd_template.cellid_quick/skeleton/skeleton.Rmd @@ -40,7 +40,8 @@ if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes") # Our lab's GitHub organizacion lives at https://github.com/darksideoftheshmoo/ -remotes::install_github("darksideoftheshmoo/rcell2-cellid") +if (!requireNamespace("rcell2.cellid", quietly = TRUE)) + remotes::install_github("darksideoftheshmoo/rcell2-cellid") ``` # Notebook Setup @@ -112,12 +113,12 @@ detailed explanation is available in the [Path to the dataset] section of this notebook. ```{r} -if(!requireNamespace("remotes")){ +if(!requireNamespace("remotes", quietly = T)){ # Install the "remotes" package if not found: install.packages("remotes") } -if(!requireNamespace("rcell2.examples")){ +if(!requireNamespace("rcell2.examples", quietly = T)){ # Install the "rcell2.examples" package if not found: remotes::install_github("darksideoftheshmoo/rcell2.examples") } @@ -253,7 +254,10 @@ cell.boundaries %>% filter(pixtype == "b") %>% ggplot(aes(x,y,color=factor(t.frame)))+ geom_path()+ - facet_wrap(~pos, scales = "free") + theme(aspect.ratio = 1) + facet_wrap(~pos, scales = "free") + theme(aspect.ratio = 1) + + theme_minimal() + + labs(color="frame") + + theme(aspect.ratio = 1) ``` > This data is only available if `cell2` has been run with `output_coords_to_tsv = T`.