Merge pull request #56 from fungenomics/dev-bhavyaa

Clusters app v1.4 update
fungenomics · Oct 29, 2021 · b61aa90 · b61aa90
2 parents e4223f0 + 7e6ce45
commit b61aa90
Show file tree

Hide file tree

Showing 10 changed files with 2,187 additions and 356 deletions.
diff --git a/LICENSE b/LICENSE
diff --git a/README.md b/README.md
@@ -30,7 +30,7 @@ and a data directory `data`.
 brain across the lifespan, based on data from the BrainSpan project
 * `clusters`: Contains the R code for the shiny app for exploring gene expression
 based on clusters from the scRNAseq atlas of the developing mouse forebrain and pons
-generated our lab
+generated by our lab
 
 
 ## Datasets which can be explored with the app

diff --git a/clusters/.gitignore b/clusters/.gitignore
@@ -16,13 +16,15 @@ data/*.Rds
 data/*.tsv
 data/*.feather
 data/*.txt
+data/*.gz
 
 data/*/*.RData
 data/*/*.Rda
 data/*/*.Rds
 data/*/*.tsv
 data/*/*.feather
 data/*/*.txt
+data/*/*.gz
 
 # Exclude illustrator files
 */img/*.ai

diff --git a/clusters/data/data.json b/clusters/data/data.json
diff --git a/clusters/data/data_prep/prep_palettes.R b/clusters/data/data_prep/prep_palettes.R
@@ -4,7 +4,7 @@ library(dplyr)
 library(readr)
 
 metadata <- data.table::fread("../joint_mouse/metadata_20190715.tsv", data.table = FALSE) %>% 
-  select(Sample, Age, Species, Structure, Alias, Cell_type, Cluster, Colour, Cell_class, N_cells) %>% 
+  select(Sample, Age, Species, Structure, Alias, Cell_type, Cluster, Colour, Cell_class, N_cells, Cluster_number) %>% 
   mutate(Cluster_nounderscore = gsub("_", " ", Cluster)) %>% 
   write_tsv("../joint_mouse/metadata_20190715_select.tsv")