---
title: "Shiny"
author: "Luise A. Seeker"
date: "18/01/2022"
output: html_document
---
```{r}
library(ShinyCell)
library(Seurat)
library(here)
library(ggsci)
```
```{r}
mypal <- pal_npg("nrc", alpha = 0.7)(10)
mypal2 <-pal_tron("legacy", alpha = 0.7)(7)
mypal3 <- pal_lancet("lanonc", alpha = 0.7)(9)
mypal4 <- pal_simpsons(palette = c("springfield"), alpha = 0.7)(16)
mypal5 <- pal_rickandmorty(palette = c("schwifty"), alpha = 0.7)(6)
mypal6 <- pal_futurama(palette = c("planetexpress"), alpha = 0.7)(5)
mypal7 <- pal_startrek(palette = c("uniform"), alpha = 0.7)(5)
mycoloursP<- c(mypal, mypal2, mypal3, mypal4, mypal5, mypal6, mypal7, "black", "blue")
```
# Complete dataset
```{r}
seu <- readRDS(here(here("data",
"single_nuc_data",
"data_for_publication",
"HCA_complete_dataset.RDS")))
scConf1 = createConfig(seu, meta.to.include = colnames(seu@meta.data)[1:42])
scConf1 = modMetaName(scConf1, meta.to.mod = c("X10XBatch",
"total_percent_mito",
"CountsPerCluster_res_0_8",
"IdCountGroup",
"samplesPerCluster_res_0_8",
"sample_count_per_cl_group",
"gender"),
new.name = c("10X_batch",
"percent_mito",
"don_ids_per_clu_0_8",
"don_ids_per_clu_0_8_gr",
"sampl_per_clu_0_8",
"sampl_per_clu_0_8_gr",
"sex"))
scConf1 = modDefault(scConf1, default1 = "cell_lineage", default2 = "Tissue")
#scConf1 = modColours(scConf1, meta.to.mod = "cluster_id",
# new.colours= mycoloursP)
makeShinyFiles(seu, scConf1, gex.assay = "RNA", gex.slot = "data",
gene.mapping = TRUE, shiny.prefix = "sc1",
shiny.dir = "shiny_app_multi/",
default.gene1 = "PLP1", default.gene2 = "SNAP25",
default.multigene = c("RBFOX1","SPARC","OPALIN","GFAP","CD74",
"SNAP25","RELN","CLDN5","PDGFRA"),
default.dimred = c("UMAP_1", "UMAP_2"))
```
# Oligodendroglia
```{r}
seu <- readRDS(here("data",
"single_nuc_data",
"oligodendroglia",
"srt_oligos_and_opcs_LS.RDS"))
scConf2 = createConfig(seu)
scConf2 = delMeta(scConf2, c("orig.ident", "BBN", "CauseOfDeath_1a",
"CauseOfDeath_1b", "CauseOfDeath_1c",
"CauseOfDeath_1d", "Cryostat_date",
"SlideBox", "Location_Block",
"comments", "RNAconcRIN",
"RINvalueDate", "RINvalueRemeasured",#
"rEeXTRACT", "project_name", "percent.mt",
"low_lib_size", "large_lib_size","low_n_features",
"high_n_features", "high_subsets_mito_percent",
"discard", "ScaterQC_failed", "seurat_clusters",
"S.Score", "G2M.Score" , "Phase", "old.ident", #
"sample_qc_failed" , "QC_UMI",
"sum",
"detected", "total", "ProcessNumber",
"CountsPerCluster_res_0_8", "IdCountGroup", ##
"samplesPerCluster_res_0_8",
"sample_count_per_cl_group", "nad_ol" , "RINvalue",
"rough_annot"
))
scConf2 = modMetaName(scConf2, meta.to.mod = c("X10XBatch",
"total_percent_mito",
"gender",
"ol_clusters_named"),
new.name = c("10X_batch",
"percent_mito",
"sex",
"cluster_id"))
scConf2 = modDefault(scConf2, default1 = "cluster_id", default2 = "Tissue")
#scConf2 = modColours(scConf2, meta.to.mod = "library",
# new.colours= c("black", "blue", "purple"))
makeShinyFiles(seu, scConf2, gex.assay = "RNA", gex.slot = "data",
gene.mapping = TRUE, shiny.prefix = "sc2",
shiny.dir = "shiny_app_multi/",
default.gene1 = "PLP1", default.gene2 = "PDGFRA",
default.multigene = c("RBFOX1","SPARC","OPALIN","FMN1","PDGFRA",
"PLP1","HNC2","NELL1","PAX3"),
default.dimred = c("UMAP_1", "UMAP_2"))
```
```{r}
seu <- readRDS(here("data",
"single_nuc_data",
"astrocytes",
"HCA_astrocytes.RDS"))
scConf3 = createConfig(seu)
scConf3 = delMeta(scConf3, c("orig.ident", "BBN", "CauseOfDeath_1a",
"CauseOfDeath_1b", "CauseOfDeath_1c",
"CauseOfDeath_1d", "Cryostat_date",
"SlideBox", "Location_Block",
"comments", "RNAconcRIN",
"RINvalueDate", "RINvalueRemeasured",#
"rEeXTRACT", "project_name", "percent.mt",
"low_lib_size", "large_lib_size","low_n_features",
"high_n_features", "high_subsets_mito_percent",
"discard", "ScaterQC_failed", "seurat_clusters",
"S.Score", "G2M.Score" , "Phase", "old.ident",
"sample_qc_failed" , "QC_UMI",
"sum",
"detected", "total", "ProcessNumber",
"CountsPerCluster_res_0_8", "IdCountGroup",
"samplesPerCluster_res_0_8",
"sample_count_per_cl_group", "RINvalue", "clusters_0.5",
"clusters_0.9" , "clusters_1", "clusters_1.1" ,
"clusters_1.2", "clusters_1.3", "clusters_1.4",
"astrocytes_clu"
))
scConf3 = modMetaName(scConf3, meta.to.mod = c("X10XBatch",
"total_percent_mito",
"gender",
"rough_annot"),
new.name = c("10X_batch",
"percent_mito",
"sex",
"cell_type"))
#scConf2 = modColours(scConf2, meta.to.mod = "library",
# new.colours= c("black", "blue", "purple"))
scConf3 = modDefault(scConf3, default1 = "cluster_id", default2 = "Tissue")
makeShinyFiles(seu, scConf3, gex.assay = "RNA", gex.slot = "data",
gene.mapping = TRUE, shiny.prefix = "sc3",
shiny.dir = "shiny_app_multi/",
default.gene1 = "GFAP", default.gene2 = "NKAIN2",
default.multigene = c("GFAP","ADGRV1","PAX3","PAK3","FAT3",
"SKAP2","BCAN","GREB1L","CPAMD8"),
default.dimred = c("UMAP_1", "UMAP_2"))
```
```{r}
seu <- readRDS(here("data",
"single_nuc_data",
"microglia",
"HCA_microglia.RDS"))
scConf4 = createConfig(seu)
scConf4 = delMeta(scConf4, c("orig.ident", "BBN", "CauseOfDeath_1a",
"CauseOfDeath_1b", "CauseOfDeath_1c",
"CauseOfDeath_1d", "Cryostat_date",
"SlideBox", "Location_Block",
"comments", "RNAconcRIN",
"RINvalueDate", "RINvalueRemeasured",#
"rEeXTRACT", "project_name", "percent.mt",
"low_lib_size", "large_lib_size","low_n_features",
"high_n_features", "high_subsets_mito_percent",
"discard", "ScaterQC_failed", "seurat_clusters",
"S.Score", "G2M.Score" , "Phase", "old.ident",
"sample_qc_failed" , "QC_UMI",
"sum",
"detected", "total", "ProcessNumber",
"CountsPerCluster_res_0_8", "IdCountGroup",
"samplesPerCluster_res_0_8",
"sample_count_per_cl_group", "RINvalue", "clusters_0.5",
"clusters_0.9" , "clusters_1", "clusters_1.1" ,
"clusters_1.2", "clusters_1.3", "clusters_1.4"
))
scConf4 = modMetaName(scConf4, meta.to.mod = c("X10XBatch",
"total_percent_mito",
"gender",
"rough_annot",
"microglia_clu"),
new.name = c("10X_batch",
"percent_mito",
"sex",
"cell_type",
"cluster_id"))
#scConf2 = modColours(scConf2, meta.to.mod = "library",
# new.colours= c("black", "blue", "purple"))
scConf4 = modDefault(scConf4, default1 = "cluster_id", default2 = "Tissue")
makeShinyFiles(seu, scConf4, gex.assay = "RNA", gex.slot = "data",
gene.mapping = TRUE, shiny.prefix = "sc4",
shiny.dir = "shiny_app_multi/",
default.gene1 = "CD74", default.gene2 = "IBA1",
default.multigene = c("HIF1A","GRID2","HLA-DRA","DDX5","PLP1",
"NEAT1","CX3CR1","CD74","IBA1"),
default.dimred = c("UMAP_1", "UMAP_2"))
```
```{r}
seu <- readRDS(here("data",
"single_nuc_data",
"vascular_cells",
"HCA_vascular_cells.RDS"))
scConf5 = createConfig(seu)
scConf5 = delMeta(scConf5, c("orig.ident", "BBN", "CauseOfDeath_1a",
"CauseOfDeath_1b", "CauseOfDeath_1c",
"CauseOfDeath_1d", "Cryostat_date",
"SlideBox", "Location_Block",
"comments", "RNAconcRIN",
"RINvalueDate", "RINvalueRemeasured",#
"rEeXTRACT", "project_name", "percent.mt",
"low_lib_size", "large_lib_size","low_n_features",
"high_n_features", "high_subsets_mito_percent",
"discard", "ScaterQC_failed", "seurat_clusters",
"S.Score", "G2M.Score" , "Phase", "old.ident",
"sample_qc_failed" , "QC_UMI",
"sum",
"detected", "total", "ProcessNumber",
"CountsPerCluster_res_0_8", "IdCountGroup",
"samplesPerCluster_res_0_8",
"sample_count_per_cl_group", "RINvalue", "clusters_0.5",
"clusters_0.9" , "clusters_1", "clusters_1.1" ,
"clusters_1.2", "clusters_1.3", "clusters_1.4"
))
scConf5 = modMetaName(scConf5, meta.to.mod = c("X10XBatch",
"total_percent_mito",
"gender",
"rough_annot",
"vascular_cells_clu"),
new.name = c("10X_batch",
"percent_mito",
"sex",
"cell_type",
"cluster_id"))
#scConf2 = modColours(scConf2, meta.to.mod = "library",
# new.colours= c("black", "blue", "purple"))
scConf5 = modDefault(scConf5, default1 = "cluster_id", default2 = "Tissue")
makeShinyFiles(seu, scConf5, gex.assay = "RNA", gex.slot = "data",
gene.mapping = TRUE, shiny.prefix = "sc5",
shiny.dir = "shiny_app_multi/",
default.gene1 = "CLDN5", default.gene2 = "NOTCH3",
default.multigene = c("CLDN5","NOTCH3","PLP1","ACTA4","HEY2",
"VGFC","MFSD2A","PDGFRB","VCAM1"),
default.dimred = c("UMAP_1", "UMAP_2"))
```
```{r}
seu <- readRDS(here("data",
"single_nuc_data",
"neurons",
"HCA_neurons.RDS"))
scConf6 = createConfig(seu)
scConf6 = delMeta(scConf6, c("orig.ident", "BBN", "CauseOfDeath_1a",
"CauseOfDeath_1b", "CauseOfDeath_1c",
"CauseOfDeath_1d", "Cryostat_date",
"SlideBox", "Location_Block",
"comments", "RNAconcRIN",
"RINvalueDate", "RINvalueRemeasured",#
"rEeXTRACT", "project_name", "percent.mt",
"low_lib_size", "large_lib_size","low_n_features",
"high_n_features", "high_subsets_mito_percent",
"discard", "ScaterQC_failed", "seurat_clusters",
"S.Score", "G2M.Score" , "Phase", "old.ident",
"sample_qc_failed" , "QC_UMI",
"sum",
"detected", "total", "ProcessNumber",
"CountsPerCluster_res_0_8", "IdCountGroup",
"samplesPerCluster_res_0_8",
"sample_count_per_cl_group", "RINvalue", "clusters_0.5",
"clusters_0.9" , "clusters_1", "clusters_1.1" ,
"clusters_1.2", "clusters_1.3", "clusters_1.4"
))
scConf6 = modMetaName(scConf6, meta.to.mod = c("X10XBatch",
"total_percent_mito",
"gender",
"rough_annot",
"neurons_clu" ),
new.name = c("10X_batch",
"percent_mito",
"sex",
"cell_type",
"cluster_id"))
#scConf2 = modColours(scConf2, meta.to.mod = "library",
# new.colours= c("black", "blue", "purple"))
scConf6 = modDefault(scConf6, default1 = "cluster_id", default2 = "Tissue")
makeShinyFiles(seu, scConf6, gex.assay = "RNA", gex.slot = "data",
gene.mapping = TRUE, shiny.prefix = "sc6",
shiny.dir = "shiny_app_multi/",
default.gene1 = "SATB2", default.gene2 = "GAD1",
default.multigene = c("SNAP25","SATB2","GAD1","RELN","CALB1",
"CALB2","PVALB","NPY","NOS1"),
default.dimred = c("UMAP_1", "UMAP_2"))
```
```{r}
citation = list(
author = "Seeker L. A. et al.",
title = "",
journal = "TBC",
volume = "TBC",
page = "TBC",
year = "TBC",
doi = "TBC",
link = "TBC")
makeShinyCodesMulti(
shiny.title = "Human white matter cell heterogeneity with region, age and sex",
shiny.footnotes = citation,
shiny.prefix = c("sc1", "sc2", "sc3", "sc4", "sc5", "sc6"),
shiny.headers = c("Complete dataset", "Oligodendroglia", "Astrocytes",
"Microglia", "Vascular cells", "Neurons"),
shiny.dir = "shiny_app_multi/")
```
```{r}
sessionInfo()
```