Merge branch 'figuredata'

DESCRIPTION

@@ -1,11 +1,11 @@
 Package: wheelP
 Type: Package
-Title: Phosphate modulation by bacterial consortia (Title Case)
-Version: 0.0.2
+Title: Designing synthetic bacterial communities for predictable plant phenotypes
+Version: 0.1.0
 Author: Sur Herrera Paredes
 Maintainer: Sur Herrera Paredes <sur00mx@gmail.com>
-Description: Code and data for analysis of the effect of bacterial blocks on plant
-    phosphate accumulation and other related plant phenotypes.
+Description: Code and data for designing synthetic bacterial communities
+    for predictable plant phenotypes.
 Imports:
     AMOR (>= 0.0-15),
     reshape2,

README.md

@@ -14,13 +14,38 @@ You will require the devtools package. Once that package is installed just type:
 devtools::install_github("surh/wheelP")
 ```
 
+# Data
+
+The raw sequence data is available in the appropriate academic repositories. RNA-seq data is at
+NCBI GEO database under accession [GSE102248](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE102248).
+Microbial 16S gene sequencing is available at the EBI SRA under accession [PRJEB22060](https://www.ebi.ac.uk/ena/data/view/PRJEB22060).
+
+All other experimental data and numeric values underlying figures in the associated manuscript
+is made available here as R package data. It can be accessed after installation using
+`data(<DATASETNAME>)` in the R console. A full description of all the available
+datasets can be found at the [DATASETS.md](DATASETS.md) file.
+
+# Scripts
+
+The [scripts directory](inst/scripts/) contains scripts used for analysis in the associated manuscript.
+The scripts follow a naming convention in which a prefix is used to indicate the general set of
+data that they analyze, and they are numbered to indicate they way in which they were run. In some
+cases, scripts with higher numbers are dependent on output from scripts with lower numbers. The prefixes
+are as follow:
+* *gc\_* corresponds to the analysis of *in vitro* bacterial growth curves.
+* *binP\_* corresponds to the analysis of plant phenotypes in plant-bacterium binary interaction assays.
+* *syncom\_* corresponds to the analysis of plant phenotypes in bacterial synthetic community assays.
+* *colonization\_* corresponds to the analysis of bacterial abundances in synthetic community assays.
+* *rna\_* corresponds to the analysis of plant transcriptomes in synthetic community assays.
+
 # Referencing
 
-If using the code of data, please reference this repository's URL, as well as the following:
+If using the code or data, please reference this repository's URL, as well as the following:
 
-Herrera Paredes S, Gao T, Law TF, Finkel OM, Mucyn T, Texeira PJPL, Salas González I,
-Feltcher ME, Powers MJ, Shank EA, Jones CD, Jojic V, Dangl JL & Castrillo G. "A simplified
-framework for dissecting complex host-microbiota interactions" (2017). *In revision*.
+\*Herrera Paredes S, \*Gao T, Law TF, Finkel OM, Mucyn T, Texeira PJPL, Salas González I,
+Feltcher ME, Powers MJ, Shank EA, Jones CD, Jojic V, Dangl JL & Castrillo G. "Design of 
+synthetic bacterial communities for predicable plant phenotypes" (2017). *In revision*.
+\*Co-first authors.
 
 # Copyright & license
 

inst/scripts/colonization_3.phylograms.r

@@ -17,7 +17,7 @@
 
 library(AMOR)
 library(wheelP)
-# setwd("~/rhizogenomics/experiments/2017/today3/")
+# setwd("~/rhizogenomics/experiments/2017/today11/")
 
 data(wheelP.mapsplit)
 Dat <- wheelP.mapsplit
@@ -30,7 +30,7 @@ Dat <- clean(Dat)
 Dat <- subset(Dat, !(Experiment %in% c("Validation1","Validation2")),
               drop = TRUE, clean = TRUE)
 
-Dat.ord <- collapse_by_taxonomy(Dat,level = 5, sepchar = ";",FUN = sum)
+Dat.ord <- collapse_by_taxonomy(Dat,level = 5, sepchar = ";",FUN = sum, Group = NULL)
 
 temp <- subset(Dat.ord, Pre.Pi == "+Pi,0.5%Suc" &
                  Pos.Pi == "100 uM,0%Suc" &
@@ -47,6 +47,9 @@ p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8) +
         strip.background = element_blank())
 p1
 ggsave("plusP_100uM.phylogram.svg",p1, width = 14, height = 4)
+dir.create("figuredata/")
+figS6B.plusP100.root <- p1$data
+save(figS6B.plusP100.root, file = "figuredata/figS6B.plusP100.root.rda")
 
 temp <- subset(Dat.ord, Pre.Pi == "+Pi,0.5%Suc" &
                  Pos.Pi == "100 uM,0%Suc" &
@@ -63,6 +66,9 @@ p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8) +
         strip.background = element_blank())
 p1
 ggsave("plusP_100uM.phylogram.agar.svg",p1, width = 14, height = 4)
+dir.create("figuredata/")
+figS6B.plusP100.agar <- p1$data
+save(figS6B.plusP100.agar, file = "figuredata/figS6B.plusP100.agar.rda")
 
 temp <- subset(Dat.ord, Pre.Pi == "+Pi,0.5%Suc" &
                  Pos.Pi == "30 uM,0%Suc" &
@@ -79,6 +85,9 @@ p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8) +
         strip.background = element_blank())
 p1
 ggsave("plusP_30uM.phylogram.svg",p1, width = 14, height = 4)
+dir.create("figuredata/")
+figS6B.plusP30.root <- p1$data
+save(figS6B.plusP30.root, file = "figuredata/figS6B.plusP30.root.rda")
 
 temp <- subset(Dat.ord, Pre.Pi == "+Pi,0.5%Suc" &
                  Pos.Pi == "30 uM,0%Suc" &
@@ -95,6 +104,9 @@ p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8) +
         strip.background = element_blank())
 p1
 ggsave("plusP_30uM.phylogram.agar.svg",p1, width = 14, height = 4)
+dir.create("figuredata/")
+figS6B.plusP30.agar <- p1$data
+save(figS6B.plusP30.agar, file = "figuredata/figS6B.plusP30.agar.rda")
 
 temp <- subset(Dat.ord, Pre.Pi == "-Pi,0.5%Suc" &
                  Pos.Pi == "100 uM,0%Suc" &
@@ -111,6 +123,9 @@ p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8) +
         strip.background = element_blank())
 p1
 ggsave("minusP_100uM.phylogram.svg",p1, width = 14, height = 4)
+dir.create("figuredata/")
+figS6B.minusP100.root <- p1$data
+save(figS6B.minusP100.root, file = "figuredata/figS6B.minusP100.root.rda")
 
 temp <- subset(Dat.ord, Pre.Pi == "-Pi,0.5%Suc" &
                  Pos.Pi == "100 uM,0%Suc" &
@@ -127,6 +142,9 @@ p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8) +
         strip.background = element_blank())
 p1
 ggsave("minusP_100uM.phylogram.agar.svg",p1, width = 14, height = 4)
+dir.create("figuredata/")
+figS6B.minusP100.agar <- p1$data
+save(figS6B.minusP100.agar, file = "figuredata/figS6B.minusP100.agar.rda")
 
 temp <- subset(Dat.ord, Pre.Pi == "-Pi,0.5%Suc" &
                  Pos.Pi == "30 uM,0%Suc" &
@@ -143,6 +161,9 @@ p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8,space = "fixed") +
         strip.background = element_blank())
 p1
 ggsave("minusP_30uM.phylogram.svg",p1, width = 14, height = 4)
+dir.create("figuredata/")
+figS6B.minusP30.root <- p1$data
+save(figS6B.minusP30.root, file = "figuredata/figS6B.minusP30.root.rda")
 
 temp <- subset(Dat.ord, Pre.Pi == "-Pi,0.5%Suc" &
                  Pos.Pi == "30 uM,0%Suc" &
@@ -159,6 +180,9 @@ p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8,space = "fixed") +
         strip.background = element_blank())
 p1
 ggsave("minusP_30uM.phylogram.agar.svg",p1, width = 14, height = 4)
+dir.create("figuredata/")
+figS6B.minusP30.agar <- p1$data
+save(figS6B.minusP30.agar, file = "figuredata/figS6B.minusP30.agar.rda")
 
 rm(Dat.ord, p1, temp)
 
@@ -184,7 +208,7 @@ Theo <- create_dataset(Tab = Tab,
                                                            levels = levels(Dat$Map$Bacteria)),
                                         row.names = syncoms),
                        Tax = Tax)
-Theo.ord <- collapse_by_taxonomy(Theo,level = 5, sepchar = ";",FUN = sum)
+Theo.ord <- collapse_by_taxonomy(Theo,level = 5, sepchar = ";",FUN = sum, Group = NULL)
 
 p1 <- phylogram(Theo.ord,facet = ~ Bacteria,nrow.legend = 8) +
   scale_fill_brewer(palette = "Paired") +
@@ -198,6 +222,9 @@ p1 <- phylogram(Theo.ord,facet = ~ Bacteria,nrow.legend = 8) +
         strip.background = element_blank())
 p1
 ggsave("theoretical.phylogram.svg",p1, width = 14, height = 4)
+dir.create("figuredata/")
+figS6B.theoretical <- p1$data
+save(figS6B.theoretical, file = "figuredata/figS6B.theoretical.rda")
 
 rm(Tab,Tax,Tax.colonization,b1,b2,p1,syncom,syncoms,Theo,Theo.ord)
 
@@ -223,6 +250,9 @@ p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 9) +
         strip.background = element_blank())
 p1
 ggsave("plusP_100uM.phylogram.blocks.svg",p1, width = 14, height = 4)
+dir.create("figuredata/")
+figS6C.plusP100.root <- p1$data
+save(figS6C.plusP100.root, file = "figuredata/figS6C.plusP100.root.rda")
 
 temp <- subset(Blocks, Pre.Pi == "+Pi,0.5%Suc" &
                  Pos.Pi == "100 uM,0%Suc" &
@@ -239,6 +269,9 @@ p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 9) +
         strip.background = element_blank())
 p1
 ggsave("plusP_100uM.phylogram.blocks.agar.svg",p1, width = 14, height = 4)
+dir.create("figuredata/")
+figS6C.plusP100.agar <- p1$data
+save(figS6C.plusP100.agar, file = "figuredata/figS6C.plusP100.agar.rda")
 
 temp <- subset(Blocks, Pre.Pi == "+Pi,0.5%Suc" &
                  Pos.Pi == "30 uM,0%Suc" &
@@ -255,6 +288,9 @@ p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 9) +
         strip.background = element_blank())
 p1
 ggsave("plusP_30uM.phylogram.blocks.svg",p1, width = 14, height = 4)
+dir.create("figuredata/")
+figS6C.plusP30.root <- p1$data
+save(figS6C.plusP30.root, file = "figuredata/figS6C.plusP30.root.rda")
 
 temp <- subset(Blocks, Pre.Pi == "+Pi,0.5%Suc" &
                  Pos.Pi == "30 uM,0%Suc" &
@@ -271,6 +307,9 @@ p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 9) +
         strip.background = element_blank())
 p1
 ggsave("plusP_30uM.phylogram.blocks.agar.svg",p1, width = 14, height = 4)
+dir.create("figuredata/")
+figS6C.plusP30.agar <- p1$data
+save(figS6C.plusP30.agar, file = "figuredata/figS6C.plusP30.agar.rda")
 
 temp <- subset(Blocks, Pre.Pi == "-Pi,0.5%Suc" &
                  Pos.Pi == "100 uM,0%Suc" &
@@ -287,6 +326,9 @@ p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 9) +
         strip.background = element_blank())
 p1
 ggsave("minusP_100uM.phylogram.blocks.svg",p1, width = 14, height = 4)
+dir.create("figuredata/")
+figS6C.minusP100.root <- p1$data
+save(figS6C.minusP100.root, file = "figuredata/figS6C.minusP100.root.rda")
 
 temp <- subset(Blocks, Pre.Pi == "-Pi,0.5%Suc" &
                  Pos.Pi == "100 uM,0%Suc" &
@@ -303,6 +345,9 @@ p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 9) +
         strip.background = element_blank())
 p1
 ggsave("minusP_100uM.phylogram.blocks.agar.svg",p1, width = 14, height = 4)
+dir.create("figuredata/")
+figS6C.minusP100.agar <- p1$data
+save(figS6C.minusP100.agar, file = "figuredata/figS6C.minusP100.agar.rda")
 
 temp <- subset(Blocks, Pre.Pi == "-Pi,0.5%Suc" &
                  Pos.Pi == "30 uM,0%Suc" &
@@ -319,6 +364,9 @@ p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 9) +
         strip.background = element_blank())
 p1
 ggsave("minusP_30uM.phylogram.blocks.svg",p1, width = 14, height = 4)
+dir.create("figuredata/")
+figS6C.minusP30.root <- p1$data
+save(figS6C.minusP30.root, file = "figuredata/figS6C.minusP30.root.rda")
 
 temp <- subset(Blocks, Pre.Pi == "-Pi,0.5%Suc" &
                  Pos.Pi == "30 uM,0%Suc" &
@@ -335,5 +383,8 @@ p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 9) +
         strip.background = element_blank())
 p1
 ggsave("minusP_30uM.phylogram.blocks.agar.svg",p1, width = 14, height = 4)
+dir.create("figuredata/")
+figS6C.minusP30.agar <- p1$data
+save(figS6C.minusP30.agar, file = "figuredata/figS6C.minusP30.agar.rda")
 
 rm(p1,Blocks,temp)

inst/scripts/colonization_4.validation_phylograms.r

@@ -32,7 +32,7 @@ Dat <- subset(Dat, (Experiment %in% c("Validation1","Validation2")),
 Dat <- subset(Dat, Fraction != "T0Agar",
               drop = TRUE, clean = TRUE)
 
-Dat.ord <- collapse_by_taxonomy(Dat,level = 5, sepchar = ";",FUN = sum)
+Dat.ord <- collapse_by_taxonomy(Dat,level = 5, sepchar = ";",FUN = sum, Group = NULL)
 
 temp <- subset(Dat.ord, Fraction == "Root")
 p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8) +
@@ -47,6 +47,9 @@ p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8) +
         strip.background = element_blank())
 p1
 ggsave("validation.phylogram.svg",p1, width = 14, height = 4)
+dir.create("figuredata/")
+figS12.order.root <- p1$data
+save(figS12.order.root, file = "figuredata/figS12.order.root.rda")
 
 temp <- subset(Dat.ord, Fraction == "Agar")
 p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8) +
@@ -61,6 +64,9 @@ p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8) +
         strip.background = element_blank())
 p1
 ggsave("validation.phylogram.agar.svg",p1, width = 14, height = 4)
+dir.create("figuredata/")
+figS12.order.agar <- p1$data
+save(figS12.order.agar, file = "figuredata/figS12.order.agar.rda")
 
 temp <- subset(Dat.ord, Fraction == "Inoculum")
 p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8) +
@@ -75,10 +81,12 @@ p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 8) +
         strip.background = element_blank())
 p1
 ggsave("validation.phylogram.inoculum.svg",p1, width = 14, height = 4)
+dir.create("figuredata/")
+figS12.order.inoc <- p1$data
+save(figS12.order.inoc, file = "figuredata/figS12.order.inoc.rda")
 
 rm(Dat.ord, p1, temp)
 
-
 #### Blocks
 Blocks <- create_dataset(Tab = collapse_matrix(Dat$Tab,
                                                groups = Dat$Tax$Block,
@@ -100,6 +108,9 @@ p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 9) +
         strip.background = element_blank())
 p1
 ggsave("validation.phylogram.blocks.svg",p1, width = 14, height = 4)
+dir.create("figuredata/")
+figS12.block.root <- p1$data
+save(figS12.block.root, file = "figuredata/figS12.block.root.rda")
 
 temp <- subset(Blocks, Fraction == "Agar")
 p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 9) +
@@ -114,6 +125,9 @@ p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 9) +
         strip.background = element_blank())
 p1
 ggsave("validation.phylogram.blocks.agar.svg",p1, width = 14, height = 4)
+dir.create("figuredata/")
+figS12.block.agar <- p1$data
+save(figS12.block.agar, file = "figuredata/figS12.block.agar.rda")
 
 temp <- subset(Blocks, Fraction == "Inoculum")
 p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 9) +
@@ -128,3 +142,6 @@ p1 <- phylogram(temp,facet = ~ Bacteria,nrow.legend = 9) +
         strip.background = element_blank())
 p1
 ggsave("validation.phylogram.blocks.inoculum.svg",p1, width = 14, height = 4)
+dir.create("figuredata/")
+figS12.block.inoc <- p1$data
+save(figS12.block.inoc, file = "figuredata/figS12.block.inoc.rda")

inst/scripts/colonization_5.ordination.r

@@ -63,4 +63,7 @@ p1 <- ggplot(Dat$Map, aes(x = MDS1, y = MDS2, col = Fraction, fill = Fraction))
 
 p1
 ggsave("colonization_mds_conditioned.svg",p1, width = 4, height = 4)
+dir.create("figuredata/")
+figS6A <- p1$data
+save(figS6A, file = "figuredata/figS6A.rda")
 

inst/scripts/rna_2.cores_previous.r

@@ -19,7 +19,7 @@ library(AMOR)
 library(wheelP)
 library(edgeR)
 
-setwd("~/rhizogenomics/experiments/2017/today7/corepi_picontent/")
+# setwd("~/rhizogenomics/experiments/2017/today11")
 # devtools::document("~/rhizogenomics/src/trunk/phosphate_code/wheelP/")
 
 data(wheelP.rna)
@@ -180,6 +180,9 @@ p1 <- ggplot(Res.sc,aes(x = Measured, y = Predicted)) +
                                   size = 22))
 p1
 ggsave('corepi.additivity.svg',p1,width = 7, height = 7)
+dir.create("figuredata/")
+fig5B <- p1$data
+save(fig5B, file = "figuredata/fig5B.rda")
 
 
 ########## Core pi vs pi content
@@ -238,6 +241,9 @@ p1 <- ggplot(subset(dat, EndP == '30 uM,0%Suc'),aes(x = Pi_content, y = core.ind
   theme_classic()
 p1
 ggsave('corepi_vs_pi.svg', p1, width = 4, height = 5)
+dir.create("figuredata/")
+figS8 <- p1$data
+save(figS8, file = "figuredata/figS8.rda")
 
 #### THE FOLLOWING SECTION IS INCORRECT!!
 #### IT CALCULATES GOODNESS OF FIT OF ADDITIVE ONLY MODEL