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Updated figures for CH1 scripts (NFix-cb) for Oecologia (as requested…
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… by editor).

Signed-off-by: Jonathan A. Whiteley <jonathan.whiteley@mail.mcgill.ca>
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@jawhiteley
jawhiteley committed Nov 4, 2012
1 parent 0044d00 commit 69660cf
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Showing 6 changed files with 23 additions and 22 deletions.
25 changes: 13 additions & 12 deletions Nfix-Cyanobacteria/2_ARA-cb_Explore.R
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Expand Up @@ -3,7 +3,7 @@
### Data Exploration
### Acetylene Reduction Assay (ARA: N-fixation)
### vs. cyanobacteria density
### Jonathan Whiteley R v2.12 2011-11-02
### Jonathan Whiteley R v2.12 2012-10-28
################################################################
## INITIALISE
################################################################
Expand Down Expand Up @@ -164,6 +164,7 @@ Spp.lines <- list(stat_smooth(aes(y=Stigonema, linetype="Stigonema"),
method="gam", se=FALSE)
)

Cyano_scaleName <- "Genus"
if (F) { # using melted df & group variable?
Cells.df <- melt(SECCa, id=c("SampleID", "Cells"),
measure=c("Hcells", "Stigonema", "Stigonema.H", "Nostoc", "Nostoc.H",
Expand All @@ -179,22 +180,22 @@ if (F) { # using melted df & group variable?
shape=variable, colour=variable, size=variable) ) +
scale_x_continuous(expand=c(0.01,0)) +
scale_y_continuous(expand=c(0.01,0)) +
scale_colour_manual(name="Species",
scale_colour_manual(name=Cyano_scaleName,
values=structure(Spp.plotMap[, "col"],
names=Spp.plotMap$Var),
breaks=Spp.plotMap[, "Var"],
labels=Spp.plotMap[, "Label"]) +
scale_size_manual(name="Species",
scale_size_manual(name=Cyano_scaleName,
values=structure(Spp.plotMap[, "size"],
names=Spp.plotMap$Var),
breaks=Spp.plotMap[, "Var"],
labels=Spp.plotMap[, "Label"]) +
scale_shape_manual(name="Species",
scale_shape_manual(name=Cyano_scaleName,
values=structure(Spp.plotMap[, "shape"],
names=Spp.plotMap$Var),
breaks=Spp.plotMap[, "Var"],
labels=Spp.plotMap[, "Label"]) +
scale_linetype_manual(name="Species",
scale_linetype_manual(name=Cyano_scaleName,
values=structure(Spp.plotMap[, "lty"],
names=Spp.plotMap$Var),
breaks=Spp.plotMap[, "Var"],
Expand All @@ -211,22 +212,22 @@ Cells.plot <- ggplot(data=SECCa, aes(x=Cells, y=Cells)) +
xlab(Cells.axlab) + ylab(Cells.units) +
scale_x_continuous(expand=c(0.01,0), formatter="format_scale", num.scale=Cells.scale) +
scale_y_continuous(expand=c(0.01,0), formatter="format_scale", num.scale=Cells.scale) +
scale_colour_manual(name="Species",
scale_colour_manual(name=Cyano_scaleName,
values=structure(Spp.plotMap[, "col"],
names=Spp.plotMap$Var),
breaks=Spp.plotMap[, "Var"],
labels=Spp.plotMap[, "Label"]) +
scale_shape_manual(name="Species",
scale_shape_manual(name=Cyano_scaleName,
values=structure(Spp.plotMap[, "shape"],
names=Spp.plotMap$Var),
breaks=Spp.plotMap[, "Var"],
labels=Spp.plotMap[, "Label"]) +
scale_size_manual(name="Species",
scale_size_manual(name=Cyano_scaleName,
values=structure(Spp.plotMap[, "size"],
names=Spp.plotMap$Var),
breaks=Spp.plotMap[, "Var"],
labels=Spp.plotMap[, "Label"]) +
scale_linetype_manual(name="Species",
scale_linetype_manual(name=Cyano_scaleName,
values=structure(Spp.plotMap[, "lty"],
names=Spp.plotMap$Var),
breaks=Spp.plotMap[, "Var"],
Expand Down Expand Up @@ -294,17 +295,17 @@ geom_point(aes(y=Stigonema.H, colour="Stigonema",
xlab(Cells.axlab) + ylab(HCells.axlab) +
scale_x_continuous(expand=c(0.01,0), formatter="format_scale", num.scale=Cells.scale) +
scale_y_continuous(expand=c(0.01,0), formatter="format_scale", num.scale=Cells.scale) +
scale_shape_manual(name="Species",
scale_shape_manual(name=Cyano_scaleName,
values=structure(Hcells.plotMap[, "shape"],
names=Hcells.plotMap$Var),
breaks=Hcells.plotMap[, "Var"],
labels=Hcells.plotMap[, "Label"]) +
scale_colour_manual(name="Species",
scale_colour_manual(name=Cyano_scaleName,
values=structure(Hcells.plotMap[, "col"],
names=Hcells.plotMap$Var),
breaks=Hcells.plotMap[, "Var"],
labels=Hcells.plotMap[, "Label"]) +
scale_size_manual(name="Species",
scale_size_manual(name=Cyano_scaleName,
values=structure(Hcells.plotMap[, "size"],
names=Hcells.plotMap$Var),
breaks=Hcells.plotMap[, "Var"],
Expand Down
4 changes: 2 additions & 2 deletions output/Results - H2O - 1.txt
View file
Expand Up @@ -5,7 +5,7 @@ Chamber: Ambient, Full Chamber
Fragmentation: Continuous, Full Corridors, Pseudo-Corridors, Isolated
Patches: Inner, other, Outer

Sun Oct 21 15:37:13 2012
Sat Oct 27 16:38:26 2012

================================================================
================ Patch scale Results =========================
Expand Down Expand Up @@ -42,7 +42,7 @@ Residuals 112 627031 5598
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

% latex table generated in R 2.12.0 by xtable 1.5-6 package
% Sun Oct 21 15:37:14 2012
% Sat Oct 27 16:38:29 2012
\begin{table}[ht]
\begin{center}
\begin{tabular}{lrrrrr}
Expand Down
4 changes: 2 additions & 2 deletions output/Results - H2O - 123.txt
View file
Expand Up @@ -5,7 +5,7 @@ Chamber: Ambient, Full Chamber
Fragmentation: Continuous, Full Corridors, Pseudo-Corridors, Isolated
Patches: Inner, other, Outer

Sun Oct 21 15:37:19 2012
Sat Oct 27 16:38:33 2012

================================================================
================ Patch scale Results =========================
Expand Down Expand Up @@ -56,7 +56,7 @@ Residuals 336 4137426 12314
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

% latex table generated in R 2.12.0 by xtable 1.5-6 package
% Sun Oct 21 15:37:22 2012
% Sat Oct 27 16:38:36 2012
\begin{table}[ht]
\begin{center}
\begin{tabular}{lrrrrr}
Expand Down
4 changes: 2 additions & 2 deletions output/Results - H2O - 2.txt
View file
Expand Up @@ -5,7 +5,7 @@ Chamber: Ambient, Full Chamber
Fragmentation: Continuous, Full Corridors, Pseudo-Corridors, Isolated
Patches: Inner, other, Outer

Sun Oct 21 15:37:15 2012
Sat Oct 27 16:38:29 2012

================================================================
================ Patch scale Results =========================
Expand Down Expand Up @@ -42,7 +42,7 @@ Residuals 112 2484940 22187
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

% latex table generated in R 2.12.0 by xtable 1.5-6 package
% Sun Oct 21 15:37:16 2012
% Sat Oct 27 16:38:30 2012
\begin{table}[ht]
\begin{center}
\begin{tabular}{lrrrrr}
Expand Down
4 changes: 2 additions & 2 deletions output/Results - H2O - 3-IO.txt
View file
Expand Up @@ -5,7 +5,7 @@ Chamber: Ambient, Full Chamber
Fragmentation: Continuous, Full Corridors, Pseudo-Corridors, Isolated
Patches: Inner, Outer

Sun Oct 21 15:37:18 2012
Sat Oct 27 16:38:32 2012

================================================================
================ Patch scale Results =========================
Expand Down Expand Up @@ -42,7 +42,7 @@ Residuals 56 508289 9077
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

% latex table generated in R 2.12.0 by xtable 1.5-6 package
% Sun Oct 21 15:37:19 2012
% Sat Oct 27 16:38:33 2012
\begin{table}[ht]
\begin{center}
\begin{tabular}{lrrrrr}
Expand Down
4 changes: 2 additions & 2 deletions output/Results - H2O - 3.txt
View file
Expand Up @@ -5,7 +5,7 @@ Chamber: Ambient, Full Chamber
Fragmentation: Continuous, Full Corridors, Pseudo-Corridors, Isolated
Patches: Inner, other, Outer

Sun Oct 21 15:37:16 2012
Sat Oct 27 16:38:30 2012

================================================================
================ Patch scale Results =========================
Expand Down Expand Up @@ -42,7 +42,7 @@ Residuals 112 1025455 9156
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

% latex table generated in R 2.12.0 by xtable 1.5-6 package
% Sun Oct 21 15:37:18 2012
% Sat Oct 27 16:38:32 2012
\begin{table}[ht]
\begin{center}
\begin{tabular}{lrrrrr}
Expand Down

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