knitr::opts_chunk$set(echo = F, error = T)
library(tidyverse)
mat_raw <- 'data-raw/external/scirep_sequential_qc.txt' %>% rexseek::read_mat() sample_class <- 'data-raw/external/scirep_classes.txt' %>% readr::read_csv(T, 'cc')
mat_raw[1:10, 1:6]
mat <- mat_raw %>% rexseek::filter_low()
mat[1:10, 1:6]
rexseek::as_SingleCellExperiment(mat, col_data = sample_class) %>% rexseek::plot_highest_exprs()
headers <- paste0( c('before', 'TMM', 'RLE', 'CPM', 'CPM top_n', 'CPM remove certain RNA type', 'CPM reference gene'), ' normalization' ) mat_norms <- list( mat, rexseek::norm_tmm(mat), rexseek::norm_rle(mat), rexseek::norm_cpm(mat), rexseek::norm_cpm_top(mat, 20), rexseek::norm_cpm_rm(mat, c('miRNA', 'piRNA')), rexseek::norm_cpm_refer(mat, rexseek::suggest_refer$id) ) report_mat <- function(...) { child_output <- knitr::knit_child( system.file('rmd/norm_report_child.Rmd', package = 'rexseek'), quiet = T, options = list(params = list(...)) ) writeLines(child_output) } purrr::pmap( list(header = headers, mat_norm = mat_norms), report_mat, sample_class = sample_class, shape = 'label', color = 'label' ) %>% invisible()
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