Comparing Rolling LCM data with TPMs

Barplots of all C4 and Calvind Cycle genes using TPMs

require(ggplot2)

## Loading required package: ggplot2

C4Hm.m <- read.csv("C4Hmmelt.csv", header=T, sep= "\t", as.is=T)
C4Hm.m$variable <-as.factor(C4Hm.m$variable)
print(levels(C4Hm.m$variable))

## [1] "BS"     "CgTOT"  "LCM_BS" "LCM_M"  "M"

C4Hm.m$variable = factor(C4Hm.m$variable, levels(C4Hm.m$variable)[c(2,3,4,1,5)])


BS <- subset(C4Hm.m, cell.x=="BS")
M<- subset(C4Hm.m, cell.x=="M")
MBS <- subset(C4Hm.m, cell.x=="M/BS")


barp <-ggplot(BS, aes(x=variable, y = value, ymin=value -SE, ymax=value +SE)) + 
  geom_bar(stat="identity", fill="goldenrod3", colour="white") +
  theme_classic()+
  geom_errorbar(width=0.25)+
  labs(title = 'Expected Bundle Sheath Enriched genes') +
  theme(strip.background = element_rect(fill = "white", colour="white"))+
  theme(strip.text.x = element_text(face = c("italic"), size = 10, hjust = 0.2, vjust = 0.1, ))+
  facet_wrap(~ C4name.x , scales="free" ) +
  ylab ("TPMs") + 
  theme( axis.title.x = element_blank()) +
  theme(aspect.ratio=0.5) 





barpm <-ggplot(M, aes(x=variable, y = value, ymin=value -SE, ymax=value +SE)) + 
  geom_bar(stat="identity", fill="firebrick4", colour="white") +
  theme_classic()+
  geom_errorbar(width=0.25)+
  labs(title = 'Expected Mesophyll Enriched genes') +
  theme(strip.background = element_rect(fill = "white", colour="white"))+
  theme(strip.text.x = element_text(face = c("italic"), size = 10, hjust = 0.2, vjust = 0.1, ))+
  facet_wrap(~ C4name.x , scales="free" ) +
  ylab ("TPMs") + 
  theme( axis.title.x = element_blank()) +
  theme(aspect.ratio=0.5) 




barpmbs <-ggplot(MBS, aes(x=variable, y = value, ymin=value -SE, ymax=value +SE)) + 
  geom_bar(stat="identity", fill="darkseagreen4", colour="white") +
  theme_classic()+
  geom_errorbar(width=0.25)+
  labs(title = 'Not yet defined cell specific genes') +
  theme(strip.background = element_rect(fill = "white", colour="white"))+
  theme(strip.text.x = element_text(face = c("italic"), size = 10, hjust = 0.2, vjust = 0.1, ))+
  facet_wrap(~ C4name.x , scales="free" ) +
  ylab ("TPMs") + 
  theme( axis.title.x = element_blank()) +
  theme(aspect.ratio=0.5) 

The plots

barp

barpm

barpmbs