Streptococcus pyogenes pharyngitis elicits diverse antibody responses to key vaccine antigens influenced by the imprint of past infections.

Here you will find the raw data (RawData.RData) and code (CHIVAS_SEROLOGY_Code.Rmd, an R Markdown file) for generating the analysis and figures for the following publication:

Streptococcus pyogenes pharyngitis elicits diverse antibody responses to key vaccine antigens influenced by the imprint of past infections.

Joshua Osowicki1,2,3 #, Hannah R Frost1 #, Kristy I Azzopardi1, Alana L Whitcombe4, Reuben McGregor4, Lauren H. Carlton4, Ciara Baker1, Loraine Fabri1,5,6, Manisha Pandey7, Michael F Good7, Jonathan R. Carapetis8,9,10, Mark J Walker11,12,13, Pierre R Smeesters1,2,5,6, Paul V Licciardi2,14, Nicole J Moreland4 *, Danika L Hill15 *, Andrew C Steer1,2,3 *

Provided in the RData file are the following items: 

Dataframes: 

"outcome" : clinical variables associated with human challenge for each participant

"data" : ELISA and functional antibody responses for human challenge participants. Each timepoint and isotype for each antigen as seperate column)

"data_long": Data equivalent to "data" file but in long format, i.e. One column for each antigen, timepoint and isotype as factors. 

"data.melt" :  Data equivalent to "data" file but in longer format , i.e. timepoint, isotype and antigen as factors, 'value' as ELISA AU. 

"luminex" : IgG responses to 6 antigens analysed by luminex bead-based assay in human challenge participants.

"luminex.children" : IgG responses to 6 antigen analysed by luminex bead-based assay in children

Vectors:

"pharyngitis" : participant "id" for the 19 individuals that developed pharyngitis. 

"Antigen.Order" : relates to "Main" antigen classification used in Figure 2

'additional" : relates to "Additional  

Function: 

"custom_theme" : used as a theme when using ggplot to graph. 

Adobe Illustrator or Inkscape were used to generate the final image files for publication, with some graph editing to axes labels, font size, adding p-values etc. 

Additional files: 

 3 .csv files have been included for download

"ELISA_data_wide_format.csv", a wide format data table of 25 human challenge individuals and 219 variables. Equivalent to the 'data' dataframe in the RData file

"CHIVAS_luminex.csv", a long format data table of 25 human challenge participants at 1 week, 1 month, and 3 months. Equivalent to the 'luminex' dataframe in the RData file. 

"Luminex.children.csv", a datatable of 6 luminex variables for 39 children (healthy and post pharyngitis). Equivalent to the 'luminex.children' dataframe in the RData file.