Leon Eyrich Jessen
This package aims at visualising output from the Barracoda 1.0 server
Using Hadley Wickham's brilliant devtools
package, we can easily install Barracoda2viz
like so:
install.packages("devtools")
devtools::install_github("leonjessen/Barracoda2viz")
Once the package has been installed, we can simply load it like so:
library("Barracoda2viz")
Additional libraries required are:
library("tidyverse")
library("readxl")
library("cowplot")
library("ggseqlogo")
library("PepTools")
The easiest way to run the package is by simply calling the workflow wrapper
d = do_barracoda_workflow(
input_xlsx = 'test_data/test_set_1.xlsx',
output_png = 'test_data/test_set_1.png')
d
## # A tibble: 4,860 x 21
## barcode sample count.1 input.1 input.2 input.3 log_fold_change
## <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 A19B62 4805 20% 1579 431 459 344 3.8411781
## 2 A20B70 4805 20% 275 104 118 90 3.3005942
## 3 A22B64 4805 20% 21 106 123 85 -0.4118250
## 4 A23B71 4805 20% 102 249 258 224 0.6361368
## 5 A25B66 4805 20% 10 111 110 89 -1.4683328
## 6 A19B61 4805 20% 4821 1246 1235 1048 3.9291584
## 7 A20B80 4805 20% 27 158 156 152 -0.6368945
## 8 A22B75 4805 20% 30 247 302 234 -1.2213967
## 9 A23B82 4805 20% 1947 484 559 453 3.8607997
## 10 A20B63 4805 20% 1784 314 381 297 4.3292026
## # ... with 4,850 more rows, and 14 more variables: p <dbl>,
## # pep.number <chr>, mut_pos <dbl>, mut_res_three <chr>,
## # mut_res_one <chr>, pep_type <chr>, p_count_1_pos <dbl>,
## # q_input_1_pos <dbl>, q_input_2_pos <dbl>, q_input_3_pos <dbl>,
## # q_input_pos_mean <dbl>, KLD_res <dbl>, KLD_pos <dbl>, KLD_height <dbl>
do_barracoda_workflow()
calls a sequence of 6 steps:
do_barracoda_workflow
## function(input_xlsx, output_png){
##
## # 1. Read raw barracoda data
## d = read_barracoda_excel(path = input_xlsx)
##
## # 2. Clean the raw barracoda data
## d_clean = d %>% clean_barracoda_data
##
## # 3. Augment barracoda data
## d_clean_aug = d_clean %>% augment_barracoda_data
##
## # 4. Compute Kullback Leibler values
## d_clean_aug_kld = d_clean_aug %>% get_KLD
##
## # 5. Create logos
## d_clean_aug_kld %>% mk_logo(path = output_png)
##
## # 6. Return final barracoda data
## return(d_clean_aug_kld)
##
## }
## <environment: namespace:Barracoda2viz>
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.