## ------------------------------------------------------------------------
.onLoad <- function(libname, pkgname) {
data("ALL_TCR_GENES",
package=pkgname, envir=parent.env(environment()))
}
PATH_TO_TABLES = file.path( "tables" )
#' @import Seurat
#' @import ggplot2
#' @import magrittr
#' @export
if( packageVersion("ggplot2") < "2.2.1.9000" ) {
warning("You may need the development version of ggplot2 if you want the
`overplot_adjust=T` option in `custom_feature_plot` to work.")
}
#' @export
get_rene_markers = function(){
markers_df = read.csv( file.path( PATH_TO_TABLES, "cell_type_markers.csv" ), stringsAsFactors = T )
if( !all( markers_df$marker == Capitalize( markers_df$marker ) ) ){
warning( paste0( "Not all genes in ",
file.path( PATH_TO_TABLES, "cell_type_markers.csv" ),
" are Capital Case." ) )
}
return( markers_df )
}
#' @export
get_ramilowski = function(){
ramilowski = read.table( file.path( PATH_TO_TABLES, "LigandReceptor_Ramilowski2015_mouse.txt" ),
header = T, sep="\t", stringsAsFactors = F )
return( ramilowski )
}
#' @export
get_macosko_cc_genes = function( case = "Capital" ){
cc_genes = read.csv( file.path( PATH_TO_TABLES, "Macosko_cell_cycle_genes.txt" ),
sep = "", header = T, stringsAsFactors=FALSE )
colnames_temp = colnames( cc_genes )
if( case == "Capital" ){
cc_genes = apply( cc_genes, MARGIN = 2, FUN = Capitalize )
} else if ( case == "UPPER" ) {
cc_genes = apply( cc_genes, MARGIN = 2, FUN = toupper )
}
colnames( cc_genes ) = colnames_temp
return ( cc_genes )
}
#' @export
get_mouse_tfs = function( capitalization = "all" ){
mouse_tfs = read.table( file.path( PATH_TO_TABLES, "mouse_tfs.txt" ), header = T )$symbol %>% as.character
if( capitalization == "all" ){
mouse_tfs = c( mouse_tfs, Capitalize( mouse_tfs ), toupper( mouse_tfs ) )
} else if( capitalization == "UPPER" ){
mouse_tfs = toupper( mouse_tfs )
} else if( capitalization == "Capitalized" ){
mouse_tfs = Capitalize( mouse_tfs )
} else if( capitalization == "unchanged" ){
# don't change it!
}
return( mouse_tfs )
}
#' @export
get_poised_genes = function(){
x = read.table( file.path( PATH_TO_TABLES, "Lesch2016_NatGen_PoisedGenes.txt" ),
header = T, stringsAsFactors = F )
return( x[["mouse_gene_symbol"]] )
}
#' @export
get_ortholog_table = function(){
ortholog_table_path = file.path( PATH_TO_TABLES, "mousegene_matchedHumanOrth.txt" )
if( !file.exists( ortholog_table_path ) ){
stop( "Please put a table of human-mouse orthologs at PATH_TO_TABLES/mousegene_matchedHumanOrth.csv. It should be a CSV file with columns named `mousesym` and `humansym` containing mouse and human gene symbols. ")
}
return( read.csv( ortholog_table_path, header = T, stringsAsFactors = F ) )
}
CC_PHASES = c("IG1.S", "S", "G2.M", "M", "M.G1")
blue_gray_red = colorspace::diverge_hcl ( 30, c = 180, l = c( 40, 80 ) )
Thanksgiving_colors = c("yellow", "orange", "red", "brown")
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