diff --git a/.Rhistory b/.Rhistory index 1827b02..0b46f0d 100644 --- a/.Rhistory +++ b/.Rhistory @@ -1,40 +1,3 @@ -scale_y_continuous(breaks=c(-3,-2, -1, 0, 1, 2, 3), limits=c(-3, 3)) + -theme(plot.margin = unit(c(2,2,2,2), "lines")) -humanendo <- annotate_figure(humanendo, fig.lab = "C", fig.lab.face = "bold", fig.lab.size = 16) -ggsave("figures/human_endomorphin1.tiff", device = "tiff") -# Human beta-Endorphin Plot -humanbe <- ggplot(humandf, aes(x = humandf$X, y = humandf$b.endorphin)) + -geom_signif(annotations = c(formatC("*"),formatC("*"), formatC("*")), y_position = c(2.5, .5, 1.5), xmin=c(1, 1, 2), xmax=c(3, 2, 3)) + -geom_errorbar(data=humandf[humandf$b.endorphin > 0,], inherit.aes = F, aes(x= humandf[humandf$b.endorphin > 0,]$X, ymin = humandf[humandf$b.endorphin > 0,]$b.endorphin, ymax = humandf[humandf$b.endorphin > 0,]$b.endorphin + humandf[humandf$b.endorphin > 0,]$b.endorphin.SEM), width = .2, color = "#9966ff", position = position_dodge(.9)) + -geom_errorbar(data=humandf[humandf$b.endorphin < 0,], inherit.aes = F, aes(x= humandf[humandf$b.endorphin < 0,]$X, ymin = humandf[humandf$b.endorphin < 0,]$b.endorphin, ymax = humandf[humandf$b.endorphin < 0,]$b.endorphin - humandf[humandf$b.endorphin < 0,]$b.endorphin.SEM), width = .2, color = "#9966ff", position = position_dodge(.9)) + -geom_bar(position = position_dodge(.01), width = 0.6, stat = "identity", fill = "#9966ff", colour="#9966ff") + -scale_x_discrete(labels = c( -"Human cAMP" = "cAMP", -"Human NFkB" = "NF-κB", -"Human JNK" = "JNK" -)) + -theme( -panel.grid.major = element_blank(), panel.grid.minor = element_blank(), -panel.background = element_blank() -) + ggtitle("β-Endorphin") + -xlab(NULL) + ylab("ΔLog(τ/KA)") + theme_pubclean() + -scale_y_continuous(breaks=c(-3,-2, -1, 0, 1, 2, 3), limits=c(-3, 3)) + -theme(plot.margin = unit(c(2,2,2,2), "lines")) -humanbe <- annotate_figure(humanbe, fig.lab = "D", fig.lab.face = "bold", fig.lab.size = 16) -ggsave("figures/human_betaendorphin.tiff", device = "tiff") -# Human TRV130 Plot -humantrv <- ggplot(humandf, aes(x = X, y = TRV130)) + -geom_signif(annotations = c(formatC("*"),formatC("*")), y_position = c(1.5, 2.5), xmin=c(1, 2), xmax=c(2, 3)) + -geom_bar(position = position_dodge(.01), width = 0.6, stat = "identity", fill = "#00b050") + -geom_errorbar(data=humandf[humandf$TRV130 > 0,], inherit.aes = F, aes(x= humandf[humandf$TRV130 > 0,]$X, ymin = humandf[humandf$TRV130 > 0,]$TRV130, ymax = humandf[humandf$TRV130 > 0,]$TRV130 + humandf[humandf$TRV130 > 0,]$TRV130.SEM), width = .2, color = "#00b050", position = position_dodge(.9)) + -geom_errorbar(data=humandf[humandf$TRV130 < 0,], inherit.aes = F, aes(x= humandf[humandf$TRV130 < 0,]$X, ymin = humandf[humandf$TRV130 < 0,]$TRV130, ymax = humandf[humandf$TRV130 < 0,]$TRV130 - humandf[humandf$TRV130 < 0,]$TRV130.SEM), width = .2, color = "#00b050", position = position_dodge(.9)) + -scale_x_discrete(labels = c( -"Human cAMP" = "cAMP", -"Human NFkB" = "NF-κB", -"Human JNK" = "JNK" -)) + -theme( -panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_blank() ) + ggtitle("TRV130") + xlab(NULL) + ylab("ΔLog(τ/KA)") + theme_pubclean() + @@ -510,3 +473,40 @@ arranged <- ggarrange(humanmor, humanmet, humanendo, humanbe, humantrv, mmmor, mmmet, mmendo, mmbe, mmtrv, common.legend = TRUE, ncol = 5, nrow = 2) ggsave("figures/arranged_plots_deltalogka.tiff", width = 15, height = 7, dpi = 450, device = "tiff") +# columns +cols <- c("Morphine", "Met.enkephalin", "endomorphin.1", "b.endorphin", "TRV130") +cols +source('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars_2019_01_25.R', encoding = 'UTF-8') +source('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars_2019_01_25.R', encoding = 'UTF-8') +source('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars_2019_01_25.R', encoding = 'UTF-8') +df <- as.data.frame(read.csv(file = "data/deltalogka_2019_01_25.csv", header = TRUE, sep = ",")) +df +source('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars_2019_01_25.R', encoding = 'UTF-8') +source('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars_2019_01_25.R', encoding = 'UTF-8') +source('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars_2019_01_25.R', encoding = 'UTF-8') +source('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars_2019_01_25.R', encoding = 'UTF-8') +source('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars_2019_01_25.R', encoding = 'UTF-8') +source('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars_2019_01_25.R', encoding = 'UTF-8') +source('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars_2019_01_25.R', encoding = 'UTF-8') +source('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars_2019_01_25.R', encoding = 'UTF-8') +source('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars_2019_01_25.R', encoding = 'UTF-8') +setwd("C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz") +source('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars_2019_01_25.R', encoding = 'UTF-8') +source('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars_2019_01_25.R', encoding = 'UTF-8') +source('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars_2019_01_25.R', encoding = 'UTF-8') +source('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars_2019_01_25.R', encoding = 'UTF-8') +source('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars_2019_01_25.R', encoding = 'UTF-8') +source('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars_2019_01_25.R', encoding = 'UTF-8') +source('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars_2019_01_25.R', encoding = 'UTF-8') +source('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars_2019_01_25.R', encoding = 'UTF-8') +source('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars_2019_01_25.R', encoding = 'UTF-8') +debugSource('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars.R', encoding = 'UTF-8') +debugSource('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars.R', encoding = 'UTF-8') +?geom_signif +debugSource('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars.R', encoding = 'UTF-8') +source('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars_2019_01_25.R', encoding = 'UTF-8') +source('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars_2019_01_25.R', encoding = 'UTF-8') +source('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars_2019_01_25.R', encoding = 'UTF-8') +source('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars_2019_01_25.R', encoding = 'UTF-8') +source('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars_2019_01_25.R', encoding = 'UTF-8') +source('C:/Users/shutchins2/Desktop/GitRepo/vallender/projects/mu-data-viz/code/delta_log_bars_2019_01_25.R', encoding = 'UTF-8') diff --git a/.Rproj.user/9BE7717F/sources/prop/INDEX b/.Rproj.user/9BE7717F/sources/prop/INDEX index ffffd14..e60c39f 100644 --- a/.Rproj.user/9BE7717F/sources/prop/INDEX +++ b/.Rproj.user/9BE7717F/sources/prop/INDEX @@ -14,8 +14,12 @@ C%3A%2FUsers%2Fshutchins2%2FDesktop%2FGitRepo%2Fvallender%2Fmisc%2Ftest%2Findex. 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+C%3A%2FUsers%2Fshutchins2%2FDesktop%2FGitRepo%2Fvallender%2Fprojects%2Fmu-data-viz%2Ftest.Rmd="8646F971" C%3A%2FUsers%2Fshutchins2%2FDesktop%2FGitRepo%2Fvallender-projects%2Fcookiecutters%2Fcookiecutter-lab-project%2F%7B%7Bcookiecutter.project_name%7D%7D%2Fanalysis%2FREADME.txt="7401CF4B" C%3A%2FUsers%2Fshutchins2%2FDesktop%2FGitRepo%2Fvallender-projects%2Fcookiecutters%2Fcookiecutter-lab-project%2F%7B%7Bcookiecutter.project_slug%7D%7D%2FREADME.txt="8DBC5741" C%3A%2FUsers%2Fshutchins2%2FDesktop%2FGitRepo%2Fvallender-projects%2Fcookiecutters%2Fcookiecutter-lab-project%2F%7B%7Bcookiecutter.project_slug%7D%7D%2Fdocs%2FREADME.txt="237176FF" diff --git a/.Rproj.user/shared/notebooks/paths b/.Rproj.user/shared/notebooks/paths index db5b913..c5a5917 100644 --- a/.Rproj.user/shared/notebooks/paths +++ b/.Rproj.user/shared/notebooks/paths @@ -6,7 +6,12 @@ C:/Users/shutchins2/Desktop/GitRepo/vallender/misc/test/_layouts/default.html="A 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