SingleR --> celldex

ComunidadBioInfo · Aug 13, 2021 · f2c7b0d · f2c7b0d
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diff --git a/02-postcards.R b/02-postcards.R
@@ -1,26 +1,26 @@
-## ---- eval=FALSE, warning=FALSE, message=FALSE--------------------------------------------
+## ---- eval=FALSE, warning=FALSE, message=FALSE--------------------------
 ## # se descargó previamente, así que solo se carga
 ## library("here") # busca la raiz del proyecto en el que se encuentre
 
 
-## ---- eval=FALSE, warning=FALSE, message=FALSE--------------------------------------------
+## ---- eval=FALSE, warning=FALSE, message=FALSE--------------------------
 ## here::here()
 
 
-## ---- eval=FALSE, warning=FALSE, message=FALSE--------------------------------------------
+## ---- eval=FALSE, warning=FALSE, message=FALSE--------------------------
 ## getwd() # regresa la path en donde nos encontramos
 ## setwd("direccion/deseada") # nos lleva a la path indicada
 
 
-## ---- eval=FALSE, warning=FALSE, message=FALSE--------------------------------------------
+## ---- eval=FALSE, warning=FALSE, message=FALSE--------------------------
 ## getwd() # para checar en donde nos encontramos
 ## here::here() # para checar dónde te encuentras
 ## 
 ## # nos movemos al subdirectorio R
 ## setwd(here::here("R")) # podemos cambiar de directorio, aun así `here está en la raíz
 
 
-## ---- eval=FALSE, warning=FALSE, message=FALSE--------------------------------------------
+## ---- eval=FALSE, warning=FALSE, message=FALSE--------------------------
 ## # como ejemplo: vamos a guardar datos en archivo y cargarlos
 ## a <- 1
 ## c <- 23
@@ -39,11 +39,11 @@
 ## list.files(here::here(), recursive = TRUE)
 
 
-## ---- eval=FALSE, warning=FALSE, message=FALSE--------------------------------------------
+## ---- eval=FALSE, warning=FALSE, message=FALSE--------------------------
 ## usethis::use_r("notas-prueba.R") # no importando en qué path estemos
 
 
-## ---- eval=FALSE, warning=FALSE, message=FALSE--------------------------------------------
+## ---- eval=FALSE, warning=FALSE, message=FALSE--------------------------
 ## # paquetes que vamos a requerir
 ## install.packages(c("gitcreds", "gert", "gh"))
 ## # cargarlos de manera separada
@@ -52,14 +52,14 @@
 ## library("gh")
 
 
-## ---- eval=FALSE, warning=FALSE, message=FALSE--------------------------------------------
+## ---- eval=FALSE, warning=FALSE, message=FALSE--------------------------
 ## # Para iniciar conexión con GitHub
 ## usethis::create_github_token() # redirige a github donde eligiras nombre especifico del token
 ## # copia el token para después ingresarlo con gitcreds_set()
 ## gitcreds::gitcreds_set() # aquí colocas el token (NO tu contraseña de github!!!)
 
 
-## ---- eval=FALSE, warning=FALSE, message=FALSE--------------------------------------------
+## ---- eval=FALSE, warning=FALSE, message=FALSE--------------------------
 ## # Configurar usuario de gitHub
 ## usethis::edit_git_config() # que abre el archivo .gitconfig
 ## # colocaremos nombre y correo de cuenta de github. SOLO borrar los # y respetar los demas espacios
@@ -68,19 +68,19 @@
 ## #   email = correodeGithub
 
 
-## ---- eval=FALSE, warning=FALSE, message=FALSE--------------------------------------------
+## ---- eval=FALSE, warning=FALSE, message=FALSE--------------------------
 ## # inicializar el repositorio de Git
 ## usethis::use_git() #
 ## 
 ## # conectar tu repositorio local de Git con los servidores de GitHub
 ## usethis::use_github()
 
 
-## ---- eval=FALSE, warning=FALSE, message=FALSE--------------------------------------------
+## ---- eval=FALSE, warning=FALSE, message=FALSE--------------------------
 ## gh::gh_whoami() # para checar cómo quedó la configuración
 
 
-## ---- eval=FALSE, warning=FALSE, message=FALSE--------------------------------------------
+## ---- eval=FALSE, warning=FALSE, message=FALSE--------------------------
 ## # escribimos un nuevo archivo, volvemos a usar here::here para especificar path
 ## writeLines("hola", here::here("R", "prueba-here.R"))
 ## # otra manera es usar use_r
@@ -99,96 +99,96 @@
 ## gert::git_push() # COMANDO IMPORTANTE
 
 
-## ----postcards_proj, eval = FALSE---------------------------------------------------------
+## ----postcards_proj, eval = FALSE---------------------------------------
 ## ## Creen el RStudio project. Es MUY importante que el usuario debe sea igual que en github
 ## usethis::create_project("Su_Usuario.github.io")
 
 
-## ----echo=FALSE, fig.cap="git user", out.width = "40%"------------------------------------
+## ----echo=FALSE, fig.cap="git user", out.width = "40%"------------------
 knitr::include_graphics("img_postcard/proyecto_github_user.png")
 
 
-## ----postcards_git, eval = FALSE----------------------------------------------------------
+## ----postcards_git, eval = FALSE----------------------------------------
 ## ## Configura Git y GitHub
 ## 
 ## # Con use_git() preguntará si desean hacer un commit, y después pedirá reiniciar Rstudio para que obtengan un nuevo botón llamado "git()"
 ## usethis::use_git()
 
 
-## ----echo=FALSE, fig.cap="button_git", out.width = "40%"----------------------------------
+## ----echo=FALSE, fig.cap="button_git", out.width = "40%"----------------
 knitr::include_graphics("img_postcard/activa_boton_git.png")
 
 
-## ----postcards_github, eval = FALSE-------------------------------------------------------
+## ----postcards_github, eval = FALSE-------------------------------------
 ## usethis::use_github()
 
 
-## ----postcards_create, eval = FALSE-------------------------------------------------------
+## ----postcards_create, eval = FALSE-------------------------------------
 ## ## Solo uno de estos, de acuerdo al templado que más les gustó
 ## postcards::create_postcard(template = "jolla")
 ## postcards::create_postcard(template = "jolla-blue")
 ## postcards::create_postcard(template = "trestles")
 ## postcards::create_postcard(template = "onofre")
 
 
-## ----postcards_git2, eval = FALSE---------------------------------------------------------
+## ----postcards_git2, eval = FALSE---------------------------------------
 ## ## Configura Git y GitHub
 ## 
 ## # Con use_git() preguntará si desean hacer un commit, y después pedirá reiniciar Rstudio para que obtengan un nuevo botón llamado "git()"
 ## usethis::use_git()
 
 
-## ----echo=FALSE, fig.cap="button_git", out.width = "40%"----------------------------------
+## ----echo=FALSE, fig.cap="button_git", out.width = "40%"----------------
 knitr::include_graphics("img_postcard/activa_boton_git.png")
 
 
-## ----echo=FALSE, fig.cap="button_branch", out.width = "40%"-------------------------------
+## ----echo=FALSE, fig.cap="button_branch", out.width = "40%"-------------
 knitr::include_graphics("img_postcard/branch.png")
 
 
-## ----echo=FALSE, fig.cap="add_file", out.width = "40%"------------------------------------
+## ----echo=FALSE, fig.cap="add_file", out.width = "40%"------------------
 knitr::include_graphics("img_postcard/add_stag.png")
 
 
-## ----echo=FALSE, fig.cap="button_git", out.width = "80%"----------------------------------
+## ----echo=FALSE, fig.cap="button_git", out.width = "80%"----------------
 knitr::include_graphics("img_postcard/commit_message.png")
 
 
-## ----postcards_pull, eval = FALSE---------------------------------------------------------
+## ----postcards_pull, eval = FALSE---------------------------------------
 ## ## Guardamos los archivos nuevos con el commit
 ## gert::git_commit_all("mensaje sobre el commit")
 ## 
 ## ## Subimos los archivos a github
 ## gert::git_push()
 
 
-## ----fawesome_yaml, eval = FALSE----------------------------------------------------------
+## ----fawesome_yaml, eval = FALSE----------------------------------------
 ## 
 ## 
 ## # Utlilizando `r fontawesome::fa("font-awesome-logo-full", fill = "forestgreen")` en código YAML
 ## 
 
 
-## ----echo=FALSE, fig.cap="y_fawesome", out.width = "40%"----------------------------------
+## ----echo=FALSE, fig.cap="y_fawesome", out.width = "40%"----------------
 knitr::include_graphics("img_postcard/yaml_awesome.png")
 
 
-## ----echo=FALSE, fig.cap="fawesome", out.width = "40%"------------------------------------
+## ----echo=FALSE, fig.cap="fawesome", out.width = "40%"------------------
 knitr::include_graphics("img_postcard/awesome.png")
 
 
-## ----fawesome_text, eval = FALSE----------------------------------------------------------
+## ----fawesome_text, eval = FALSE----------------------------------------
 ## 
 ## 
 ## # Utlilizando `r fontawesome::fa("font-awesome-logo-full", fill = "forestgreen")` en el texto
 ## 
 
 
-## ----echo=FALSE, fig.cap="tfawesome", out.width = "40%"-----------------------------------
+## ----echo=FALSE, fig.cap="tfawesome", out.width = "40%"-----------------
 knitr::include_graphics("img_postcard/text_awesome.png")
 
 
-## -----------------------------------------------------------------------------------------
+## -----------------------------------------------------------------------
 ## Información de la sesión de R
 Sys.time()
 proc.time()

diff --git a/04-estructura_datos.R b/04-estructura_datos.R
@@ -1,4 +1,4 @@
-## ---- warning=FALSE, message=FALSE------------------------------------------------------------------
+## ---- warning=FALSE, message=FALSE--------------------------------------
 library("scRNAseq")
 sce.416b <- LunSpikeInData(which = "416b")
 
@@ -233,7 +233,7 @@ sizeFactors(sce) <- scater::librarySizeFactors(sce)
 head(sizeFactors(sce))
 
 
-## ---------------------------------------------------------------------------------------------------
+## -----------------------------------------------------------------------
 # Creamos un data.frame
 df <- data.frame(x = c(TRUE, FALSE, NA, NA), y = c(12, 34, 56, 78))
 row.names(df) <- letters[1:4]
@@ -266,7 +266,7 @@ bool_info <- df$y < 20 | df$y > 60
 df[bool_info, ]
 
 
-## ---------------------------------------------------------------------------------------------------
+## -----------------------------------------------------------------------
 library("SingleCellExperiment")
 library("scRNAseq")
 
@@ -282,17 +282,17 @@ col.data <- DataFrame(read.csv(archivo_colData, row.names = 1, header = TRUE, ch
 row.data <- read.csv(archivo_rowData, row.names = 1, header = TRUE, check.names = F)
 
 
-## ---------------------------------------------------------------------------------------------------
+## -----------------------------------------------------------------------
 int_gen <- c("Angpt1", "Chic2", "Mir503", "Magee2", "Nenf", "Eps15l1", "Hsf2bp", "Gnptg", "Vegfb", "Atmin", "Gad1", "Gad2", "Slc32a1", "Dner", "Slc2a13", "Slc6a1", "Nrxn3")
 
 
-## ---- eval= FALSE-----------------------------------------------------------------------------------
+## ---- eval= FALSE-------------------------------------------------------
 ## library("scater")
 ## 
 ## plotHeatmap(object = tej_min_sce, features = rownames(tej_min_sce), order_columns_by = "level1class")
 
 
-## ---------------------------------------------------------------------------------------------------
+## -----------------------------------------------------------------------
 sce <- SingleCellExperiment(
     assays = list(counts = counts),
     colData = col.data,
@@ -304,30 +304,30 @@ sce <- scater::logNormCounts(sce)
 sce
 
 
-## ---------------------------------------------------------------------------------------------------
+## -----------------------------------------------------------------------
 bool_data <- rownames(rowData(sce))
 min_sce <- sce[bool_data %in% int_gen, ]
 
 
-## ---------------------------------------------------------------------------------------------------
+## -----------------------------------------------------------------------
 tej_int <- min_sce$level1class == "interneurons"
 tej_pyr <- min_sce$level1class == "pyramidal CA1"
 
 
 tej_min_sce <- min_sce[, tej_int | tej_pyr]
 
 
-## ---------------------------------------------------------------------------------------------------
+## -----------------------------------------------------------------------
 library("scater")
 
 plotHeatmap(object = tej_min_sce, features = rownames(tej_min_sce), order_columns_by = "level1class")
 
 
-## ---------------------------------------------------------------------------------------------------
+## -----------------------------------------------------------------------
 int_gen <- c("ENSMUSG00000071076", "ENSMUSG00000002076", "ENSMUSG00000024962", "ENSMUSG00000031224", "ENSMSG00000036560", "ENSMUSG00000037499", "ENSMUSG00000006276", "ENSMUSG00000035521", "ENSMUSG00000047388", "ENSMUSG0000051079", "ENSMUSG00000076122", "ENSMUSG00000029229", "ENSMUSG00000022309", "ENSMUSG00000036766", "ENSMUSG00000070880", "ENSMUSG00000026787", "ENSMUSG00000066392", "ENSMUSG00000036298", "ENSMUSG00000037771", "ENSMUSG00000030310")
 
 
-## ---------------------------------------------------------------------------------------------------
+## -----------------------------------------------------------------------
 # Descarga datos de ejemplo procesados con CellRanger
 # Paréntesis: al usar BiocFileCache solo tenemos que descargar
 #             los datos una vez.
@@ -466,7 +466,7 @@ lun.sce
 lobstr::obj_size(lun.sce) / 1024^2 ## En MB
 
 
-## ---------------------------------------------------------------------------------------------------
+## -----------------------------------------------------------------------
 ## Información de la sesión de R
 Sys.time()
 proc.time()