In MyersGroup/testisAtlas: testisAtlas: R functions and analysis scripts used in the analysis of testis single cell RNAseq

tmp <- rbind(
data.table(Expression=dnorm(seq(0,10,0.01), 4, 1)*10, Transcriptional_Programme="A"),
data.table(Expression=dnorm(seq(0,10,0.01), 5.5, 0.5)*6, Transcriptional_Programme="B"),
data.table(Expression=dexp(seq(10.6,0.6,-0.01), 1)*10, Transcriptional_Programme="C"),
data.table(Expression=dlnorm(seq(0.4,10.4,0.01), log(5), log(3))*10, Transcriptional_Programme="D"),
data.table(Expression=dbeta(seq(0.1,1.1,0.001), 4, 2.5, ncp = 0.2), Transcriptional_Programme="E"))

tmp <- cbind(tmp, "Time"=seq(0,10,0.01))

pdf("results/simulated_programme.pdf", height = 9/2, width = 16/2)
ggplot(tmp, aes(Time, Expression, colour=Transcriptional_Programme)) +
        geom_line(size=1) +
        theme_classic(base_size = 15) +
        scale_color_brewer(palette='Set1') +
        scale_x_continuous(breaks=c(0,2,4,6,8,10))+
        theme(legend.position="bottom",
              panel.grid.major = element_blank(),
              panel.grid.minor = element_blank())
dev.off()

# tmp_norm <- tmp[,.(Transcriptional_Programme, Expression=Expression/sum(Expression)),by=PseudoTime]
# 
# ggplot(tmp_norm, aes(PseudoTime,Expression, colour=Transcriptional_Programme)) +
#         geom_col() +
#         theme_classic(base_size = 15) +
#         scale_colour_brewer(palette='Set3') +
#         scale_x_continuous(expand=c(0,0), breaks=c(0,2,4,6,8,10))+
#         scale_y_continuous(expand=c(0,0), labels = scales::percent)+
#         theme(legend.position="bottom",
#               panel.grid.major = element_blank(),
#               panel.grid.minor = element_blank())

MyersGroup/testisAtlas documentation built on Nov. 29, 2020, 9:21 p.m.