Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
fig.width = 8,
fig.height = 8
)
## ---- echo = FALSE,fig.asp=0.6------------------------------------------------
library(png)
library(grid)
path_intro <- system.file("extdata", "auto.png", package = "MACSQuantifyR")
intro <- readPNG(path_intro)
grid.raster(intro)
## ----load---------------------------------------------------------------------
library(MACSQuantifyR)
library(knitr)
library(grid)
library(gridExtra)
library(png)
suppressMessages(library(R.utils))
## ----load_file, include = TRUE------------------------------------------------
file <- system.file("extdata", "drugs.xlsx",
package = "MACSQuantifyR")
## ----echo=FALSE---------------------------------------------------------------
print(basename(file))
## ----echo=FALSE,include=FALSE-------------------------------------------------
MACSQuant <- load_MACSQuant(file)
my_data <- slot(MACSQuant, "my_data")
## ----echo=FALSE---------------------------------------------------------------
kable(head(my_data), digits = 4)
## ----eval=FALSE---------------------------------------------------------------
# MACSQuant <- pipeline(filepath = file,
# sheet_name = NULL, # optional
# number_of_replicates = 3,
# number_of_conditions = 8,
# control = T)
## ---- echo = FALSE------------------------------------------------------------
example_path <- system.file("extdata/",
"plate_template_pipeline.png",
package = "MACSQuantifyR")
example_image <- readPNG(example_path)
grid.raster(example_image)
## ----echo = FALSE-------------------------------------------------------------
printf(paste("...To quit press ESC...\n",
"...You can now select your conditions",
"replicates (without control condition replicates)...\n",
" --> 18 conditions:...1...2...3...4...5...6...7...8...OK\n",
" --> Done: replicates identified\n",
" --> Done: statistics on each condition replicates\n",
"...You can now select your control replicates...\n",
" --> 1 control: ...OK...\n",
" --> Done: statistics on each control replicates\n",
"--> Done: replicates stored in variable my_replicates_sorted\n",
sep = " "))
## ----echo = FALSE-------------------------------------------------------------
warning(paste("In order_data(sorted_matrix_final, my_data, save.files =",
"save.files) : \n !!! A2 not selected and will be ignored",
sep = " "))
## ---- echo=FALSE--------------------------------------------------------------
drugs_R_image <- system.file("extdata",
"drugs.RDS",
package = "MACSQuantifyR")
MACSQuant <- readRDS(drugs_R_image)
kable(slot(MACSQuant, "statistics"), digits = 4)
## ---- echo = FALSE, fig.width=20, fig.height=20,fig.asp=0.5-------------------
example_res1 <- system.file("extdata/",
"barplot_counts_pipeline.png",
package = "MACSQuantifyR")
example_res2 <- system.file("extdata/",
"barplot_percent_pipeline.png",
package = "MACSQuantifyR")
img4 <- rasterGrob(as.raster(readPNG(example_res1)), interpolate = FALSE)
img5 <- rasterGrob(as.raster(readPNG(example_res2)), interpolate = FALSE)
grid.arrange(img4, img5, ncol = 2)
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.