Visualizing Titers

Stefan Avey

2017-05-18

Format titer data

library(titer)

head(Year1_Titers)
##   SubjectID AgeGroup              Strain Pre Post
## 1    101005    Young A California 7 2009   4  256
## 2    101005    Young     A Perth 16 2009   4   64
## 3    101005    Young  B Brisbane 60 2008  16  512
## 4    101008    Older A California 7 2009   4    4
## 5    101008    Older     A Perth 16 2009   4    4
## 6    101008    Older  B Brisbane 60 2008  64   64
titer_list <- FormatTiters(Year1_Titers)
## - Log transforming Pre and Post columns
## - Setting any negative log fold changes to 0
lapply(titer_list, head)
## $`A California 7 2009`
##   SubjectID AgeGroup              Strain Pre Post FC
## 1    101008    Older A California 7 2009   2    2  0
## 2    101011    Older A California 7 2009   2    2  0
## 3    101022    Older A California 7 2009   2    2  0
## 4    101050    Older A California 7 2009   2    3  1
## 5    101076    Older A California 7 2009   2    3  1
## 6    101015    Older A California 7 2009   2    4  2
## 
## $`A Perth 16 2009`
##   SubjectID AgeGroup          Strain Pre Post FC
## 1    101008    Older A Perth 16 2009   2    2  0
## 2    101021    Older A Perth 16 2009   2    2  0
## 3    101082    Young A Perth 16 2009   2    2  0
## 4    101022    Older A Perth 16 2009   2    3  1
## 5    101032    Older A Perth 16 2009   2    4  2
## 6    101041    Older A Perth 16 2009   2    4  2
## 
## $`B Brisbane 60 2008`
##   SubjectID AgeGroup             Strain Pre Post FC
## 1    101115    Young B Brisbane 60 2008   2    4  2
## 2    101078    Young B Brisbane 60 2008   2    5  3
## 3    101092    Young B Brisbane 60 2008   2    5  3
## 4    101119    Young B Brisbane 60 2008   2    5  3
## 5    101105    Young B Brisbane 60 2008   3    3  0
## 6    101015    Older B Brisbane 60 2008   3    4  1

Bar plots

Bar plots can show the raw data, baseline and day 28 titer values for each subject.

## Bar plot of B strain
Barplot(titer_list["A Perth 16 2009"])

## Bar plot of all strains
Barplot(titer_list, groupVar = "AgeGroup")

Bubble Charts

Bubble Charts show the relationship between baseline titer and fold change. In general, a negative slope is observed.

## Bubble Charts for all strains
BubbleChart(titer_list)

## Bubble Chart for B strain
BubbleChart(titer_list["A Perth 16 2009"])

## Add an exponential fit and color by age group
BubbleChart(titer_list["A Perth 16 2009"], fit = "exp",
            colorBy = "AgeGroup", eqSize = 5)