diff --git a/3_Analysis/.DS_Store b/3_Analysis/.DS_Store index a2a6aea..80e0c89 100644 Binary files a/3_Analysis/.DS_Store and b/3_Analysis/.DS_Store differ diff --git a/3_Analysis/Analyze.Rmd b/3_Analysis/Analyze.Rmd index 814f74e..aa29283 100644 --- a/3_Analysis/Analyze.Rmd +++ b/3_Analysis/Analyze.Rmd @@ -43,40 +43,40 @@ Main Figures: 3. 000_Figure_4.pdf 4. 000_Figure_5.pdf -Additional Files: -1. 000_Additional_File_4.html -2. 000_Additional_File_5.html -3. 000_Additional_File_6.html -4. 000_Additional_File_7.pdf -5. 000_Additional_File_8.pdf -6. 000_Additional_File_9.html -7. 000_Additional_File_10.html -8. 000_Additional_File_11.html -9. 000_Additional_File_12.html -10. 000_Additional_File_13.html -11. 000_Additional_File_14.html -12. 000_Additional_File_15.pdf -13. 000_Additional_File_16.html -14. 000_Additional_File_17.pdf -15. 000_Additional_File_18.html -16. 000_Additional_File_19.pdf -17. 000_Additional_File_20.html -18. 000_Additional_File_21.pdf -19. 000_Additional_File_22.html -20. 000_Additional_File_23.pdf -21. 000_Additional_File_24.html -22. 000_Additional_File_25.pdf -23. 000_Additional_File_26.html -24. 000_Additional_File_27.pdf +Supplemental files: +1. 000_Supplemental_Table_S4.html +2. 000_Supplemental_Table_S5.html +3. 000_Supplemental_Table_S6.html +4. 000_Supplemental_Figure_S1.pdf +5. 000_Supplemental_Figure_S2.pdf +6. 000_Supplemental_Table_S7.html +7. 000_Supplemental_Table_S8.html +8. 000_Supplemental_Table_S9.html +9. 000_Supplemental_Table_S10.html +10. 000_Supplemental_Table_S11.html +11. 000_Supplemental_Table_S12.html +12. 000_Supplemental_Figure_S3.pdf +13. 000_Supplemental_Table_S13.html +14. 000_Supplemental_Figure_S4.pdf +15. 000_Supplemental_Table_S14.html +16. 000_Supplemental_Figure_S5.pdf +17. 000_Supplemental_Table_S15.html +18. 000_Supplemental_Figure_S6.pdf +19. 000_Supplemental_Table_S16.html +20. 000_Supplemental_Figure_S7.pdf +21. 000_Supplemental_Table_S17.html +22. 000_Supplemental_Figure_S8.pdf +23. 000_Supplemental_Table_S18.html +24. 000_Supplemental_Figure_S9.pdf * Figure_1, is not output by this script; it is manually created in excel -* Table_1 is not created directly from this script, but is built from outputs associated with Additional Files 14:27. +* Table_1 is not created directly from this script, but is built from outputs associated with Supplemental figures S3:S9 and Supplemental tables S12:S18 -* Additional Files 1, 2, and 3 are created by hand in excel and are not created by this script +* Supplemental files 1, 2, and 3 are created by hand in excel and are not created by this script -* Additional_File_4 is output with raw p-values, but values are converted to fdr for publication and presented in an xlsx format document. Additional_File_12 is output with raw 2-sided test p-values, but values are converted to 1-sided (higher) and fdr for publication and presented in an xlsx format document. +* Supplemental_Table_S4 is output with raw p-values, but values are converted to fdr for publication and presented in an xlsx format document. Supplemental_Table_S10 is output with raw 2-sided test p-values, but values are converted to 1-sided (higher) and fdr for publication and presented in an xlsx format document. *** @@ -197,7 +197,7 @@ paste0("RsMSE = ", # ----------------------------------------------------------------------------- # model output ----------------------------------------------------------------- -tab_model(mymod, digits = 5, digits.p = 8, show.stat = T, wrap.labels = 100, file = "000_Additional_File_4.html") +tab_model(mymod, digits = 5, digits.p = 8, show.stat = T, wrap.labels = 100, file = "000_Supplemental_Table_S4.html") # ----------------------------------------------------------------------------- # create temporary plotting dataframe ----------------------------------------- @@ -225,7 +225,7 @@ myhighlight <- "black" myfillapha <- 0.35 myptalpha <- 0.35 mylinealpha <- 0.35 -mypalette <- setpalette +mypalette <- c("#28bd90", "#6e3001") mytextsize <- 8 myheight <- 3.345 @@ -387,7 +387,7 @@ p_b # figure output --------------------------------------------------------------- grid.arrange(p_a, p_b, nrow = 2) -pdf(file = "000_Additional_File_7.pdf", width = mywidth, height = myheight); grid.arrange(p_a, p_b, nrow = 2); dev.off() # 2columns wide, half as tall +pdf(file = "000_Supplemental_Figure_S1.pdf", width = mywidth, height = myheight); grid.arrange(p_a, p_b, nrow = 2); dev.off() # 2columns wide, half as tall # ----------------------------------------------------------------------------- rm(cc, myt, p_a, p_b, cc001, cc002, r001, r002, myx2, mybinwidth, myc, myfillapha, myheight, myhighlight, mylinealpha, myptalpha, myr, mytextsize, mytitle, mywidth, myx, myxlab, myylab) # remove the temporary variable @@ -440,7 +440,7 @@ myhighlight <- "grey50" myfillapha <- 0.35 myptalpha <- 0.35 mylinealpha <- 0.35 -mypalette <- setpalette +mypalette <- mypalette <- c("#28bd90", "#6e3001") mytextsize <- 8 myheight <- 7 @@ -468,7 +468,7 @@ p # ----------------------------------------------------------------------------- # figure output --------------------------------------------------------------- -pdf(file = "000_Additional_File_8.pdf", width = mywidth, height = myheight); p; dev.off() # 7by7 +pdf(file = "000_Supplemental_Figure_S2.pdf", width = mywidth, height = myheight); p; dev.off() # 7by7 # ----------------------------------------------------------------------------- rm(faevo.1.ce, faevo.1.cc, faevo.2.ce, faevo.2.cc, myt1, myt1r, myt2, myt2r, myt, mytr, p) # clean up this section. @@ -489,7 +489,7 @@ plot(mymod) # model fit (multi) -- looks pretty good. # ----------------------------------------------------------------------------- # model output ----------------------------------------------------------------- -tab_model(mymod, digits = 5, digits.p = 8, show.stat = T, wrap.labels = 100, file = "000_Additional_File_12.html") # table does not have corrected p-values. +tab_model(mymod, digits = 5, digits.p = 8, show.stat = T, wrap.labels = 100, file = "000_Supplemental_Table_S10.html") # table does not have corrected p-values. # ----------------------------------------------------------------------------- # create results dataframe ---------------------------------------------------- @@ -573,7 +573,7 @@ myhighlight3 <- setpalette[2] myfillapha <- 0.25 myptalpha <- 0.35 mylinealpha <- 0.35 -mypalette <- setpalette +mypalette <- mypalette <- c("#28bd90", "#6e3001") mytextsize <- 8 myheight <- 3.345 @@ -705,7 +705,7 @@ car::vif(mymod) # VIF looks okay. summary(mymod) # model output -----------------------------------------------------------------= -tab_model(mymod, digits = 5, digits.p = 8, show.stat = T, wrap.labels = 100, show.r2 = F, file = "000_Additional_File_11.html") # r2 on the lm version of htis model is +tab_model(mymod, digits = 5, digits.p = 8, show.stat = T, wrap.labels = 100, show.r2 = F, file = "000_Supplemental_Table_S9.html") # r2 on the lm version of htis model is # ----------------------------------------------------------------------------- rm(mymod) ``` @@ -907,7 +907,7 @@ for(i in 1:nrow(mypower)){ # model output ----------------------------------------------------------------- mypower2 <- round(mypower[,1:5], digits = 5) -tab_df(mypower2, file = "000_Additional_File_5.html") +tab_df(mypower2, file = "000_Supplemental_Table_S5.html") # ----------------------------------------------------------------------------- @@ -969,7 +969,7 @@ for(i in 1:nrow(mypower)){ # model output ----------------------------------------------------------------- mypower2 <- round(mypower[,1:5], digits = 5) -tab_df(mypower2, file = "000_Additional_File_6.html") +tab_df(mypower2, file = "000_Supplemental_Table_S6.html") # ----------------------------------------------------------------------------- # # plot ----------------------- @@ -1034,7 +1034,7 @@ for(i in 1:nrow(mypower)){ # model output ----------------------------------------------------------------- mypower2 <- round(mypower[,1:5], digits = 5) -tab_df(mypower2, file = "000_Additional_File_9.html") +tab_df(mypower2, file = "000_Supplemental_Table_S7.html") # ----------------------------------------------------------------------------- # # Plotting ------------------------------------------------- @@ -1098,7 +1098,7 @@ for(i in 1:nrow(mypower)){ # model output ----------------------------------------------------------------- mypower2 <- round(mypower[,1:5], digits = 5) -tab_df(mypower2, file = "000_Additional_File_10.html") +tab_df(mypower2, file = "000_Supplemental_Table_S8.html") # ----------------------------------------------------------------------------- # myheight <- 7 @@ -1271,7 +1271,7 @@ p<-ggplot(mypower, aes(x=fitchange, y=power, group=exp)) + geom_point(x = 0.05, y = pwr.t.test(d = 0.05 / psd250, n = 4, sig.level = 0.05)$power, pch = 1, size = 5, color = "gray")+ geom_point(x = 0.1, y = pwr.t.test(d = 0.1 / psd250, n = 4, sig.level = 0.05)$power, pch = 1, size = 5, color = "gray")+ scale_x_continuous(name = "Fitness difference (& fitness change) \n for individual barcodes \n ", breaks = c(0.01, 0.025, 0.05, 0.1), labels = c("1%", "2.5%", "5%", "10%"), limits = c(0,0.1))+ - scale_color_manual(values =setpalette) + + scale_color_manual(values = c("#28bd90", "#6e3001")) + labs(color = "Experiment")+ theme_classic()+ labs(tag ="A")+ @@ -1388,7 +1388,7 @@ p<-ggplot(mypower, aes(x=f2, y=power, group=exp)) + 0.5, 0.75, 1.0, 1.25, 1.5, 1.75, 2), labels = c("0.05%","", "0.25%", "0.5%", "0.75%", "1.0%", "1.25%", "1.5%", "1.75%", "2.0%"))+ - scale_color_manual(values =setpalette) + + scale_color_manual(values = c("#28bd90", "#6e3001")) + theme(legend.position = "none")+ theme(axis.text.x = element_text(angle = 45, hjust = 1)) pB <- p @@ -1425,7 +1425,7 @@ my <- myfa[order(myfa$bctID),] # placeholder dataframe # model & diagnostic plots ---------------------------------------------------- mymod <- lmer(I(scale(deltafit)) ~ I(scale(ccdeltafit)) +treatment +(1|bctID), weights = rdeltafit, data = my, control=lmerControl(optimizer ="bobyqa",optCtrl=list(maxfun=2e4))) # model output -----------------------------------------------------------------= -tab_model(mymod, digits = 5, digits.p = 8, show.stat = T, wrap.labels = 100, show.r2 = F, file = "000_Additional_File_13.html") +tab_model(mymod, digits = 5, digits.p = 8, show.stat = T, wrap.labels = 100, show.r2 = F, file = "000_Supplemental_Table_S11.html") # ----------------------------------------------------------------------------- @@ -1557,7 +1557,7 @@ summary(mymod)$adj.r.squared # for adjusted R2 value # ----------------------------------------------------------------------------- # model output ----------------------------------------------------------------- -tab_model(mymod, digits = 5, digits.p = 8, show.stat = T, wrap.labels = 100, file = "000_Additional_File_14.html") +tab_model(mymod, digits = 5, digits.p = 8, show.stat = T, wrap.labels = 100, file = "000_Supplemental_Table_S12.html") # ----------------------------------------------------------------------------- # Visualize ------------------------------------------------------------------- @@ -1607,7 +1607,7 @@ p # ----------------------------------------------------------------------------- # figure output --------------------------------------------------------------- -pdf(file = "000_Additional_File_15.pdf", width = mywidth, height = myheight); p; dev.off() +pdf(file = "000_Supplemental_Figure_S3.pdf", width = mywidth, height = myheight); p; dev.off() # ----------------------------------------------------------------------------- rm(my, mymod, p, myc, myfill, myheight, myoutline, mypalette, myptalpha, myptsize, myr, mytextsize, mytitle, mywidth, myx, myxlab, myy, myylab) @@ -1636,7 +1636,7 @@ summary(mymod)$adj.r.squared # for adjusted R2 value # ----------------------------------------------------------------------------- # model output ----------------------------------------------------------------- -tab_model(mymod, digits = 5, digits.p = 8, show.stat = T, wrap.labels = 100, file = "000_Additional_File_16.html") +tab_model(mymod, digits = 5, digits.p = 8, show.stat = T, wrap.labels = 100, file = "000_Supplemental_Table_S13.html") # ----------------------------------------------------------------------------- # Visualize ------------------------------------------------------------------- @@ -1688,7 +1688,7 @@ p # ----------------------------------------------------------------------------- # figure output --------------------------------------------------------------- -pdf(file = "000_Additional_File_17.pdf", width = mywidth, height = myheight); p; dev.off() +pdf(file = "000_Supplemental_Figure_S4.pdf", width = mywidth, height = myheight); p; dev.off() # ----------------------------------------------------------------------------- rm(my, mymod, p, myc, myfill, myheight, myoutline, mypalette, myptalpha, myptsize, myr, mytextsize, mytitle, mywidth, myx, myxlab, myy, myylab, myfillapha, mylinealpha) @@ -1717,7 +1717,7 @@ summary(mymod)$adj.r.squared # for adjusted R2 value # ----------------------------------------------------------------------------- # model output ----------------------------------------------------------------- -tab_model(mymod, digits = 5, digits.p = 8, show.stat = T, wrap.labels = 100, file = "000_Additional_File_18.html") +tab_model(mymod, digits = 5, digits.p = 8, show.stat = T, wrap.labels = 100, file = "000_Supplemental_Table_S14.html") # ----------------------------------------------------------------------------- # Visualize ------------------------------------------------------------------- @@ -1767,7 +1767,7 @@ p # ----------------------------------------------------------------------------- # figure output --------------------------------------------------------------- -pdf(file = "000_Additional_File_19.pdf", width = mywidth, height = myheight); p; dev.off() +pdf(file = "000_Supplemental_Figure_S5.pdf", width = mywidth, height = myheight); p; dev.off() # ----------------------------------------------------------------------------- rm(my, mymod, p, myc, myfill, myheight, myoutline, mypalette, myptalpha, myptsize, myr, mytextsize, mytitle, mywidth, myx, myxlab, myy, myylab) @@ -1796,7 +1796,7 @@ summary(mymod)$adj.r.squared # for adjusted R2 value # ----------------------------------------------------------------------------- # model output ----------------------------------------------------------------- -tab_model(mymod, digits = 5, digits.p = 8, show.stat = T, wrap.labels = 100, file = "000_Additional_File_20.html") +tab_model(mymod, digits = 5, digits.p = 8, show.stat = T, wrap.labels = 100, file = "000_Supplemental_Table_S15.html") # ----------------------------------------------------------------------------- @@ -1847,7 +1847,7 @@ p # ----------------------------------------------------------------------------- # figure output --------------------------------------------------------------- -pdf(file = "000_Additional_File_21.pdf", width = mywidth, height = myheight); p; dev.off() +pdf(file = "000_Supplemental_Figure_S6.pdf", width = mywidth, height = myheight); p; dev.off() # ----------------------------------------------------------------------------- rm(my, mymod, p, myc, myfill, myheight, myoutline, mypalette, myptalpha, myptsize, myr, mytextsize, mytitle, mywidth, myx, myxlab, myy, myylab) @@ -1873,7 +1873,7 @@ summary(mymod)$adj.r.squared # for adjusted R2 value # ----------------------------------------------------------------------------- # model output ----------------------------------------------------------------- -tab_model(mymod, digits = 5, digits.p = 8, show.stat = T, wrap.labels = 100, file = "000_Additional_File_22.html") +tab_model(mymod, digits = 5, digits.p = 8, show.stat = T, wrap.labels = 100, file = "000_Supplemental_Table_S16.html") # ----------------------------------------------------------------------------- # Visualize ------------------------------------------------------------------- @@ -1922,7 +1922,7 @@ p # ----------------------------------------------------------------------------- # figure output --------------------------------------------------------------- -pdf(file = "000_Additional_File_23.pdf", width = mywidth, height = myheight); p; dev.off() +pdf(file = "000_Supplemental_Figure_S7.pdf", width = mywidth, height = myheight); p; dev.off() # ----------------------------------------------------------------------------- rm(my, mymod, p, myc, myfill, myheight, myoutline, mypalette, myptalpha, myptsize, myr, mytextsize, mytitle, mywidth, myx, myxlab, myy, myylab) ``` @@ -1946,7 +1946,7 @@ summary(mymod)$adj.r.squared # for adjusted R2 value # ----------------------------------------------------------------------------- # model output ----------------------------------------------------------------- -tab_model(mymod, digits = 5, digits.p = 8, show.stat = T, wrap.labels = 100, file = "000_Additional_File_24.html") +tab_model(mymod, digits = 5, digits.p = 8, show.stat = T, wrap.labels = 100, file = "000_Supplemental_Table_S17.html") # ----------------------------------------------------------------------------- # Visualize ------------------------------------------------------------------- @@ -1996,7 +1996,7 @@ p # ----------------------------------------------------------------------------- # figure output --------------------------------------------------------------- -pdf(file = "000_Additional_File_25.pdf", width = mywidth, height = myheight); p; dev.off() +pdf(file = "000_Supplemental_Figure_S8.pdf", width = mywidth, height = myheight); p; dev.off() # ----------------------------------------------------------------------------- rm(my, mymod, p, myc, myfill, myheight, myoutline, mypalette, myptalpha, myptsize, myr, mytextsize, mytitle, mywidth, myx, myxlab, myy, myylab) ``` @@ -2024,7 +2024,7 @@ summary(mymod)$adj.r.squared # for adjusted R2 value # ----------------------------------------------------------------------------- # model output ----------------------------------------------------------------- -tab_model(mymod, digits = 5, digits.p = 8, show.stat = T, wrap.labels = 100, file = "000_Additional_File_26.html") +tab_model(mymod, digits = 5, digits.p = 8, show.stat = T, wrap.labels = 100, file = "000_Supplemental_Table_S18.html") # ----------------------------------------------------------------------------- # Visualize ------------------------------------------------------------------- @@ -2074,7 +2074,7 @@ p # ----------------------------------------------------------------------------- # figure output --------------------------------------------------------------- -pdf(file = "000_Additional_File_27.pdf", width = mywidth, height = myheight); p; dev.off() +pdf(file = "000_Supplemental_Figure_S9.pdf", width = mywidth, height = myheight); p; dev.off() # ----------------------------------------------------------------------------- rm(my, mymod, p, myc, myfill, myheight, myoutline, mypalette, myptalpha, myptsize, myr, mytextsize, mytitle, mywidth, myx, myxlab, myy, myylab) ```