plotLP-2013-11-13-WT-vs-MAVS-STING-pre-GCA.R

# Template for pre_GCA plots

library(dplyr)

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
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##     filter, lag

## The following objects are masked from 'package:base':
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##     intersect, setdiff, setequal, union

library(tidyr)
library(ggplot2)
library(readr)
source('C:/Users/kmaciag/Desktop/IRF3 Paper - Local/GCA/ggThemeLPinfection.R')

d0 <- read_csv("C:/Users/kmaciag/Desktop/IRF3 Paper - Local/GCA/2013-11-13 WT vs MAVS STING pre-GCA.csv")

## Parsed with column specification:
## cols(
##   Timept = col_double(),
##   IFNgTiming = col_character(),
##   IFNgStim = col_character(),
##   Genotype = col_character(),
##   BiolRepl = col_double(),
##   TechRep1 = col_double(),
##   TechRep2 = col_double(),
##   TechRep3 = col_double(),
##   TechRep4 = col_double(),
##   TechRep5 = col_double(),
##   TechRep6 = col_double(),
##   TechRep7 = col_double(),
##   TechRep8 = col_double(),
##   TechRep9 = col_double(),
##   TechRep10 = col_double()
## )

d <- d0 %>% gather(TechRep, lumi, -Timept, -Genotype, -IFNgTiming, -IFNgStim, -BiolRepl)  # melt data
d$Timept <- as.numeric(gsub("[^0-9.]", "", d$Timept))  # delete "hpi" text if present in data table
d <- d[d$Timept!=60,]   # exclude selected timepoints
d$log10bact <- log(d$lumi,10)  # log transform base 10

noIFNg_rows <- which(d$IFNgStim=="0U")  # Save the no-IFNg data

# Factorize. Note that assigning "labels" actually changes values
d$Genotype <- factor(d$Genotype, c("WT","MAVS", "STING"))
d$IFNgTiming<- factor(d$IFNgTiming, c("pre","post", "both"), labels=c(bquote(atop(IFN*gamma*phantom(0)*stim,'prior to infection')), bquote(atop(IFN*gamma*phantom(0)*stim,'during infection')), "both"))   #, bquote(atop(IFN*gamm*phantom(0)*stim,'both prior to and during infection'))))
d$IFNgStim <- factor(d$IFNgStim, c("0U","3U", "10U", "100U"), labels=c(expression(paste("No IFN",gamma)),expression(paste("3 U/ml IFN",gamma)),expression(paste("10 U/ml IFN", gamma)),expression(paste("100 U/ml IFN", gamma))))

# other graphic settings
theme_set(ggThemeLPinfection())

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## Attaching package: 'scales'

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## You have loaded plyr after dplyr - this is likely to cause problems.
## If you need functions from both plyr and dplyr, please load plyr first, then dplyr:
## library(plyr); library(dplyr)

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## 
## Attaching package: 'plyr'

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##     summarize

## Warning: package 'Cairo' was built under R version 4.0.3

## Warning: `panel.margin` is deprecated. Please use `panel.spacing` property
## instead

MAVS_STINGPalette <- c("#000000", "#E69F00", "#56B4E9")  # MAVS/STING KO stay orange and light blue
palette <- MAVS_STINGPalette
GenotypeLegend <- c("C57BL/6J", expression(paste(italic("MAVS"^"-/-"))), expression(paste(italic("STING"^"-/-"))))

# Plot log luminescence data facetted by IFNg stim
ggplot(d, aes(Timept, log10bact, color=Genotype)) + 
  geom_point(aes(), size=1, position=position_dodge(width = 0.5)) +
  scale_color_manual(values=palette, labels=GenotypeLegend) +
  labs(x="Time after infection (hours)", y=paste("Bacterial growth","(log10 bioluminescence)", sep='\n'), linetype="Blocking Ab") + 
  annotate("segment", x=-Inf, xend=Inf, y=-Inf, yend=-Inf)+annotate("segment", x=-Inf, xend=-Inf, y=-Inf, yend=Inf) +
  scale_y_continuous(breaks=pretty_breaks(),expand=c(0,1)) +
  guides(color = guide_legend(order = 1), linetype = guide_legend(order = 2)) +
  coord_cartesian(clip = "off") +
  facet_grid(IFNgTiming ~ IFNgStim, labeller=label_parsed)

## Warning: Removed 1083 rows containing missing values (geom_point).

# Plot No IFNg facet only combining pre+post
ggplot(d[noIFNg_rows,], aes(Timept, log10bact, color=Genotype)) + 
  geom_point(aes(), size=1, position=position_dodge(width = 0.5)) +
  scale_color_manual(values=palette, labels=GenotypeLegend) +
  labs(x="Time after infection (hours)", y=paste("Bacterial growth","(log10 bioluminescence)", sep='\n'), linetype="Blocking Ab") + 
  annotate("segment", x=-Inf, xend=Inf, y=-Inf, yend=-Inf)+annotate("segment", x=-Inf, xend=-Inf, y=-Inf, yend=Inf) +
  scale_y_continuous(breaks=pretty_breaks(),expand=c(0,1)) +
  ggtitle(expression(paste("No IFN",gamma)))

## Warning: Removed 1 rows containing missing values (geom_point).