Commit f09db416 authored by mcariou's avatar mcariou
Browse files

update doc

parent e095e5eb
......@@ -378,6 +378,8 @@ file<-file[grep(x=file, pattern="aln")]
tmp<-ifelse(rownames(tab) %in% tmprownames, 1, 0)
tab[,subrepcurrent]<-tmp
} else {
tab[,subrepcurrent]<-rep(0, nrow(tab))
}
}
@
......@@ -399,7 +401,7 @@ barplot(vectgene, horiz=TRUE, las=2)
\subsection{Concatenate and Supertree}
\subsection{Concatenate}
<<tree, fig.height=12>>=
treepath<-paste0(home, "fasta/78Lp_V2/cat.phylip_phyml_tree")
......@@ -407,6 +409,44 @@ treepath<-paste0(home, "fasta/78Lp_V2/cat.phylip_phyml_tree")
tree<-read.tree(treepath)
plot(root(tree, outgroup = "Coxiella_burnetii"))
@
<<heatmap, fig.height=12, fig.width=9>>=
library(reshape)
library(ggplot2)
dat <- data.frame(weather=c("Rain","Hail","Sunny"), Germany = c(0,1,0), Italy = c(1,0,0))
melt.data<-melt(dat, id.vars="weather", variable_name="country")
tab$species<-rownames(tab)
melt.tab<-melt(tab, id.vars="species", variable_name="gene")
#v<-c("Q5ZYP1_lpg0331","Q5ZYN4_lpg0338")
head(melt.tab)
melt.tab<-melt.tab[(melt.tab$gene %in% v)==FALSE,]
qplot(data=melt.tab,
x=gene,
y=species,
fill=factor(value),
geom="tile")+
scale_fill_manual(values=c("0"="white", "1"="red")) +
theme(axis.text.x = element_text(angle = 90))
@
<<heatmap2, fig.height=12, fig.width=9>>=
qplot(data=melt.tab,
x=species,
y=gene,
fill=factor(value),
geom="tile") +
scale_fill_manual(values=c("0"="white", "1"="red")) +
theme(axis.text.x = element_text(angle = 90))
@
\end{document}
......
......@@ -27,4 +27,4 @@
\@writefile{toc}{\contentsline {subsection}{\numberline {2.1}Get sequences from Burstein et al.}{12}{subsection.2.1}}
\@writefile{toc}{\contentsline {section}{\numberline {3}Phylogeny}{13}{section.3}}
\@writefile{toc}{\contentsline {subsection}{\numberline {3.1}Genes alignement}{13}{subsection.3.1}}
\@writefile{toc}{\contentsline {subsection}{\numberline {3.2}Concatenate and Supertree}{20}{subsection.3.2}}
\@writefile{toc}{\contentsline {subsection}{\numberline {3.2}Concatenate}{20}{subsection.3.2}}
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entering extended mode
restricted \write18 enabled.
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......@@ -833,45 +833,45 @@ n\OT1/cmtt/m/n/10.95 t"[][],[] []fill[][]=[][]TRUE[][],[] []header[][]=[][]TRUE
[]
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[]\OT1/cmtt/m/n/10.95 ## Species ATCC.number Strain.designation
Isolation ORF.prefix[]
Isolation ORF.prefix Accession[]
[]
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[]\OT1/cmtt/m/n/10.95 ## 1 L. adelaidensis ATCC49625 ATCC49625 Wa
ter in cooling tower (Adelaide, Australia) Lade[]
ter in cooling tower (Adelaide, Australia) Lade LNKA00000000[]
[]
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[]\OT1/cmtt/m/n/10.95 ## 2 L. anisa ATCC35292 WA-316-C3
Tap water (Los Angeles, CA, USA) Lani[]
Tap water (Los Angeles, CA, USA) Lani LNXS00000000 []
[]
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[]\OT1/cmtt/m/n/10.95 ## 3 L. birminghamensis ATCC43702 CDC#1407-AL-14
Lung biopsy (Alabama, USA) Lbir[]
Lung biopsy (Alabama, USA) Lbir LNXT00000000 []
[]
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[]\OT1/cmtt/m/n/10.95 ## 4 L. bozemanii ATCC33217 WIGA
Lung tissue (Key West, FL, USA) Lboz[]
Lung tissue (Key West, FL, USA) Lboz LNXU00000000 []
[]
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[]\OT1/cmtt/m/n/10.95 ## 5 L. brunensis ATCC43878 ATCC43878
Cooling tower water (Czechoslovakia) Lbru[]
Cooling tower water (Czechoslovakia) Lbru LNXV00000000 []
[]
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[]\OT1/cmtt/m/n/10.95 ## 6 L. cherrii ATCC35252 ORW
Thermally altered water (Minnesota, USA) Lche[]
Thermally altered water (Minnesota, USA) Lche LNXW00000000 []
[]
[2]
......@@ -1252,9 +1252,9 @@ ii Legionella tucsonensis Legionella waltersii[]
[]
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[]\OT1/cmtt/m/n/10.95 ## 73 Levels: Aquicella lusitana Aquicella siphonis Burkh
olderia cepacia ... Rickettsiella grylli[]
olderia cepacia Burkholderia mallei ... Rickettsiella grylli[]
[]
......@@ -1378,9 +1378,9 @@ Burkholderia cepacia[]
[]
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[]\OT1/cmtt/m/n/10.95 ## 73 Levels: Aquicella lusitana Aquicella siphonis Burkh
olderia cepacia ... Rickettsiella grylli[]
olderia cepacia Burkholderia mallei ... Rickettsiella grylli[]
[]
......@@ -1467,9 +1467,9 @@ Legionella wadsworthii[]
[]
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[]\OT1/cmtt/m/n/10.95 ## 73 Levels: Aquicella lusitana Aquicella siphonis Burkh
olderia cepacia ... Rickettsiella grylli[]
olderia cepacia Burkholderia mallei ... Rickettsiella grylli[]
[]
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[] []\OT1/cmtt/m/n/10.95 fasta[][]<-[][]read.dna[][]([][]paste0[][](aln,
[] []"/"[][],subrepcurrent,[] []"/"[][], file),[] []format[][]=[][]"fasta"[][],
[] []as.character[][]=[][]TRUE[][])[][]
[]
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[] []\OT1/cmtt/m/n/10.95 tmprownames[][]<-[][]ifelse[][]([][]grepl[][]([
][]rownames[][](fasta),[] []pattern[] []=[] []"pneumo"[][]),[][]
[]
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[] []\OT1/cmtt/m/n/10.95 substr[][]([][]rownames[][](fasta)[[][]grep
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[],[][]31[][]),[][]
[]
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[] []\OT1/cmtt/m/n/10.95 sapply[][]([][]rownames[][](fasta),[] []fun
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[]=[][]TRUE[][])[[[][]1[][]]][[][]1[][]]))[][]
[]
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[] []\OT1/cmtt/m/n/10.95 fasta[][]<-[][]read.dna[][]([][]paste0[][](aln,
[] []"/"[][],subrepcurrent,[] []"/"[][], file),[] []format[][]=[][]"fasta"[][],
[] []as.character[][]=[][]TRUE[][])[][]
[]
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[] []\OT1/cmtt/m/n/10.95 tmprownames[][]<-[][]ifelse[][]([][]grepl[][]([
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[]
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[] []\OT1/cmtt/m/n/10.95 substr[][]([][]rownames[][](fasta)[[][]grep[][]
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[] []\OT1/cmtt/m/n/10.95 sapply[][]([][]rownames[][](fasta),[] []functio
n[][]([][]x[][])[] []strsplit[][](x,[] []split[][]=[][]"."[][],[] []fixed[][]=[
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[][]\OT1/cmtt/m/n/10.95 dat[] []<-[] []data.frame[][]([][]weather[][]=[][]c[][]
([][]"Rain"[][],[][]"Hail"[][],[][]"Sunny"[][]),[] []Germany[] []=[] []c[][]([]
[]0[][],[][]1[][],[][]0[][]),[] []Italy[] []=[] []c[][]([][]1[][],[][]0[][],[][
]0[][]))[][]
[]
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[][]\OT1/cmtt/m/n/10.95 melt.data[][]<-[][]melt[][](dat,[] []id.vars[][]=[][]"w
eather"[][],[] []variable_name[][]=[][]"country"[][])[][]
[]
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......@@ -9,4 +9,4 @@
\BOOKMARK [2][-]{subsection.2.1}{Get sequences from Burstein et al.}{section.2}% 9
\BOOKMARK [1][-]{section.3}{Phylogeny}{}% 10
\BOOKMARK [2][-]{subsection.3.1}{Genes alignement}{section.3}% 11
\BOOKMARK [2][-]{subsection.3.2}{Concatenate and Supertree}{section.3}% 12
\BOOKMARK [2][-]{subsection.3.2}{Concatenate}{section.3}% 12
......@@ -141,20 +141,20 @@ We chose to use the 78 genes selected by Burstein et al. 2016. The first objecti
\hlkwd{head}\hlstd{(tab1)}
\end{alltt}
\begin{verbatim}
## Species ATCC.number Strain.designation Isolation ORF.prefix
## 1 L. adelaidensis ATCC49625 ATCC49625 Water in cooling tower (Adelaide, Australia) Lade
## 2 L. anisa ATCC35292 WA-316-C3 Tap water (Los Angeles, CA, USA) Lani
## 3 L. birminghamensis ATCC43702 CDC#1407-AL-14 Lung biopsy (Alabama, USA) Lbir
## 4 L. bozemanii ATCC33217 WIGA Lung tissue (Key West, FL, USA) Lboz
## 5 L. brunensis ATCC43878 ATCC43878 Cooling tower water (Czechoslovakia) Lbru
## 6 L. cherrii ATCC35252 ORW Thermally altered water (Minnesota, USA) Lche
## Accession Version BioSample BioProject
## 1 LNKA00000000 LNKA01000000 SAMN03842654 PRJNA285910
## 2 LNXS00000000  LNXS01000000  SAMN04274764 PRJNA285910
## 3 LNXT00000000  LNXT01000000  SAMN04274765 PRJNA285910
## 4 LNXU00000000  LNXU01000000  SAMN04274766 PRJNA285910
## 5 LNXV00000000  LNXV01000000  SAMN04274767 PRJNA285910
## 6 LNXW00000000  LNXW01000000  SAMN04274768 PRJNA285910
## Species ATCC.number Strain.designation Isolation ORF.prefix Accession
## 1 L. adelaidensis ATCC49625 ATCC49625 Water in cooling tower (Adelaide, Australia) Lade LNKA00000000
## 2 L. anisa ATCC35292 WA-316-C3 Tap water (Los Angeles, CA, USA) Lani LNXS00000000 
## 3 L. birminghamensis ATCC43702 CDC#1407-AL-14 Lung biopsy (Alabama, USA) Lbir LNXT00000000 
## 4 L. bozemanii ATCC33217 WIGA Lung tissue (Key West, FL, USA) Lboz LNXU00000000 
## 5 L. brunensis ATCC43878 ATCC43878 Cooling tower water (Czechoslovakia) Lbru LNXV00000000 
## 6 L. cherrii ATCC35252 ORW Thermally altered water (Minnesota, USA) Lche LNXW00000000 
## Version BioSample BioProject
## 1 LNKA01000000 SAMN03842654 PRJNA285910
## 2 LNXS01000000  SAMN04274764 PRJNA285910
## 3 LNXT01000000  SAMN04274765 PRJNA285910
## 4 LNXU01000000  SAMN04274766 PRJNA285910
## 5 LNXV01000000  SAMN04274767 PRJNA285910
## 6 LNXW01000000  SAMN04274768 PRJNA285910
\end{verbatim}
\end{kframe}
\end{knitrout}
......@@ -306,7 +306,7 @@ Which species are present in gupta not in the previous datasets.
## [25] Legionella rubrilucens Legionella sainthelensi Legionella santicrucis Legionella spiritensis
## [29] Legionella steelei Legionella steigerwaltii Legionella tucsonensis Legionella waltersii
## [33] Legionella worsleiensis
## 73 Levels: Aquicella lusitana Aquicella siphonis Burkholderia cepacia ... Rickettsiella grylli
## 73 Levels: Aquicella lusitana Aquicella siphonis Burkholderia cepacia Burkholderia mallei ... Rickettsiella grylli
\end{verbatim}
\begin{alltt}
\hlcom{# Only in Gupta}
......@@ -333,7 +333,7 @@ Which species are present in gupta not in the previous datasets.
## [35] Candidatus Rickettsiella viridis Rickettsiella grylli
## [37] Candidatus Berkiella aquae Candidatus Berkiella cookevillensis
## [39] Burkholderia mallei Burkholderia cepacia
## 73 Levels: Aquicella lusitana Aquicella siphonis Burkholderia cepacia ... Rickettsiella grylli
## 73 Levels: Aquicella lusitana Aquicella siphonis Burkholderia cepacia Burkholderia mallei ... Rickettsiella grylli
\end{verbatim}
\begin{alltt}
\hlcom{# only in Burstein}
......@@ -373,7 +373,7 @@ Final list: Remove Legionella drozanskii and Legionella shakespearei and Aquicel
## [17] Legionella saoudiensis Legionella taurinensis
## [19] Legionella tunisiensis Legionella wadsworthii
## [21] Legionella yabuuchiae
## 73 Levels: Aquicella lusitana Aquicella siphonis Burkholderia cepacia ... Rickettsiella grylli
## 73 Levels: Aquicella lusitana Aquicella siphonis Burkholderia cepacia Burkholderia mallei ... Rickettsiella grylli
\end{verbatim}
\begin{alltt}
\hlcom{## Keep only legio and coxiella}
......@@ -643,19 +643,17 @@ Représenter le nombre de gènes obtenus par espèces, et le nombre d'espèces p
\hlstd{subrep}
\end{alltt}
\begin{verbatim}
## [1] "Q5ZRF4_lpg2928" "Q5ZRP4_lpg2836" "Q5ZRQ7_lpg2823" "Q5ZRT6_lpg2792" "Q5ZRV3_lpg2773" "Q5ZRV4_lpg2772"
## [7] "Q5ZRV6_lpg2770" "Q5ZRW1_lpg2765" "Q5ZRX2_lpg2754" "Q5ZRZ3_lpg2727" "Q5ZS05_lpg2714" "Q5ZS08_lpg2711"
## [13] "Q5ZS49_lpg2670" "Q5ZS63_lpg2656" "Q5ZS65_lpg2654" "Q5ZT28_lpg2337" "Q5ZT35_lpg2330" "Q5ZT51_lpg2314"
## [19] "Q5ZT61_lpg2304" "Q5ZT63_lpg2302" "Q5ZTX1_lpg2037" "Q5ZTX7_lpg2031" "Q5ZU05_lpg2003" "Q5ZU96_lpg1911"
## [25] "Q5ZUH7_lpg1821" "Q5ZUJ7_lpg1801" "Q5ZUM6_lpg1767" "Q5ZUS0_lpg1722" "Q5ZUS8_lpg1714" "Q5ZUT0_lpg1712"
## [31] "Q5ZVH3_lpg1467" "Q5ZVJ6_lpg1444" "Q5ZVJ7_lpg1443" "Q5ZVL5_lpg1425" "Q5ZVP0_lpg1400" "Q5ZVP1_lpg1399"
## [37] "Q5ZVU2_lpg1348" "Q5ZVV6_lpg1334" "Q5ZVY2_lpg1306" "Q5ZWA4_lpg1181" "Q5ZWZ6_lpg0937" "Q5ZXE5_lpg0786"
## [43] "Q5ZXJ7_lpg0734" "Q5ZXK6_lpg0725" "Q5ZXL2_lpg0719" "Q5ZXN3_lpg0698" "Q5ZXP3_lpg0688" "Q5ZXP6_lpg0685"
## [49] "Q5ZXZ2_lpg0588" "Q5ZY30_lpg0543" "Q5ZY59_lpg0513" "Q5ZY67_lpg0505" "Q5ZY69_lpg0503" "Q5ZYH2_lpg0400"
## [55] "Q5ZYL9_lpg0353" "Q5ZYM1_lpg0351" "Q5ZYM4_lpg0348" "Q5ZYM6_lpg0346" "Q5ZYM7_lpg0345" "Q5ZYM8_lpg0344"
## [61] "Q5ZYM9_lpg0343" "Q5ZYN1_lpg0341" "Q5ZYN4_lpg0338" "Q5ZYN6_lpg0336" "Q5ZYN7_lpg0335" "Q5ZYN8_lpg0334"
## [67] "Q5ZYP0_lpg0332" "Q5ZYP1_lpg0331" "Q5ZYP2_lpg0330" "Q5ZYP3_lpg0329" "Q5ZYP4_lpg0328" "Q5ZYP7_lpg0325"
## [73] "Q5ZYQ0_lpg0322" "Q5ZYQ3_lpg0319" "Q5ZYQ4_lpg0318" "Q5ZYQ5_lpg0317" "Q5ZYS4_lpg0287"
## [1] "Q5ZRF4_lpg2928" "Q5ZRP4_lpg2836" "Q5ZRQ7_lpg2823" "Q5ZRT6_lpg2792" "Q5ZRV3_lpg2773" "Q5ZRV4_lpg2772" "Q5ZRV6_lpg2770"
## [8] "Q5ZRW1_lpg2765" "Q5ZRX2_lpg2754" "Q5ZRZ3_lpg2727" "Q5ZS05_lpg2714" "Q5ZS08_lpg2711" "Q5ZS49_lpg2670" "Q5ZS63_lpg2656"
## [15] "Q5ZS65_lpg2654" "Q5ZT28_lpg2337" "Q5ZT35_lpg2330" "Q5ZT51_lpg2314" "Q5ZT61_lpg2304" "Q5ZT63_lpg2302" "Q5ZTX1_lpg2037"
## [22] "Q5ZTX7_lpg2031" "Q5ZU05_lpg2003" "Q5ZU96_lpg1911" "Q5ZUH7_lpg1821" "Q5ZUJ7_lpg1801" "Q5ZUM6_lpg1767" "Q5ZUS0_lpg1722"
## [29] "Q5ZUS8_lpg1714" "Q5ZUT0_lpg1712" "Q5ZVH3_lpg1467" "Q5ZVJ6_lpg1444" "Q5ZVJ7_lpg1443" "Q5ZVL5_lpg1425" "Q5ZVP0_lpg1400"
## [36] "Q5ZVP1_lpg1399" "Q5ZVU2_lpg1348" "Q5ZVV6_lpg1334" "Q5ZVY2_lpg1306" "Q5ZWA4_lpg1181" "Q5ZWZ6_lpg0937" "Q5ZXE5_lpg0786"
## [43] "Q5ZXJ7_lpg0734" "Q5ZXK6_lpg0725" "Q5ZXL2_lpg0719" "Q5ZXN3_lpg0698" "Q5ZXP3_lpg0688" "Q5ZXP6_lpg0685" "Q5ZXZ2_lpg0588"
## [50] "Q5ZY30_lpg0543" "Q5ZY59_lpg0513" "Q5ZY67_lpg0505" "Q5ZY69_lpg0503" "Q5ZYH2_lpg0400" "Q5ZYL9_lpg0353" "Q5ZYM1_lpg0351"
## [57] "Q5ZYM4_lpg0348" "Q5ZYM6_lpg0346" "Q5ZYM7_lpg0345" "Q5ZYM8_lpg0344" "Q5ZYM9_lpg0343" "Q5ZYN1_lpg0341" "Q5ZYN4_lpg0338"
## [64] "Q5ZYN6_lpg0336" "Q5ZYN7_lpg0335" "Q5ZYN8_lpg0334" "Q5ZYP0_lpg0332" "Q5ZYP1_lpg0331" "Q5ZYP2_lpg0330" "Q5ZYP3_lpg0329"
## [71] "Q5ZYP4_lpg0328" "Q5ZYP7_lpg0325" "Q5ZYQ0_lpg0322" "Q5ZYQ3_lpg0319" "Q5ZYQ4_lpg0318" "Q5ZYQ5_lpg0317" "Q5ZYS4_lpg0287"
\end{verbatim}
\begin{alltt}
\hlstd{cat}\hlkwb{<-}\hlkwd{vector}\hlstd{()}
......@@ -780,6 +778,8 @@ Représenter le nombre de gènes obtenus par espèces, et le nombre d'espèces p
\hlstd{tmp}\hlkwb{<-}\hlkwd{ifelse}\hlstd{(}\hlkwd{rownames}\hlstd{(tab)} \hlopt{%in%} \hlstd{tmprownames,} \hlnum{1}\hlstd{,} \hlnum{0}\hlstd{)}
\hlstd{tab[,subrepcurrent]}\hlkwb{<-}\hlstd{tmp}
\hlstd{\}} \hlkwa{else} \hlstd{\{}
\hlstd{tab[,subrepcurrent]}\hlkwb{<-}\hlkwd{rep}\hlstd{(}\hlnum{0}\hlstd{,} \hlkwd{nrow}\hlstd{(tab))}
\hlstd{\}}
\hlstd{\}}
\end{alltt}
......@@ -812,7 +812,7 @@ Représenter le nombre de gènes obtenus par espèces, et le nombre d'espèces p
\subsection{Concatenate and Supertree}
\subsection{Concatenate}
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
......@@ -826,6 +826,61 @@ Représenter le nombre de gènes obtenus par espèces, et le nombre d'espèces p
\includegraphics[width=\maxwidth]{figure/tree-1}
\end{knitrout}
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlkwd{library}\hlstd{(reshape)}
\hlkwd{library}\hlstd{(ggplot2)}
\hlstd{dat} \hlkwb{<-} \hlkwd{data.frame}\hlstd{(}\hlkwc{weather}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"Rain"}\hlstd{,}\hlstr{"Hail"}\hlstd{,}\hlstr{"Sunny"}\hlstd{),} \hlkwc{Germany} \hlstd{=} \hlkwd{c}\hlstd{(}\hlnum{0}\hlstd{,}\hlnum{1}\hlstd{,}\hlnum{0}\hlstd{),} \hlkwc{Italy} \hlstd{=} \hlkwd{c}\hlstd{(}\hlnum{1}\hlstd{,}\hlnum{0}\hlstd{,}\hlnum{0}\hlstd{))}
\hlstd{melt.data}\hlkwb{<-}\hlkwd{melt}\hlstd{(dat,} \hlkwc{id.vars}\hlstd{=}\hlstr{"weather"}\hlstd{,} \hlkwc{variable_name}\hlstd{=}\hlstr{"country"}\hlstd{)}
\hlstd{tab}\hlopt{$}\hlstd{species}\hlkwb{<-}\hlkwd{rownames}\hlstd{(tab)}
\hlstd{melt.tab}\hlkwb{<-}\hlkwd{melt}\hlstd{(tab,} \hlkwc{id.vars}\hlstd{=}\hlstr{"species"}\hlstd{,} \hlkwc{variable_name}\hlstd{=}\hlstr{"gene"}\hlstd{)}
\hlcom{#v<-c("Q5ZYP1_lpg0331","Q5ZYN4_lpg0338")}
\hlkwd{head}\hlstd{(melt.tab)}
\end{alltt}
\begin{verbatim}
## species gene value
## 1 Legionella_pneumophila.AE017354 Q5ZRF4_lpg2928 1
## 2 Legionella_bozemanae Q5ZRF4_lpg2928 1
## 3 Legionella_wadsworthii Q5ZRF4_lpg2928 1
## 4 Legionella_norrlandica Q5ZRF4_lpg2928 1
## 5 Legionella_rowbothamii Q5ZRF4_lpg2928 1
## 6 Fluoribacter_gormanii Q5ZRF4_lpg2928 1
\end{verbatim}
\begin{alltt}
\hlstd{melt.tab}\hlkwb{<-}\hlstd{melt.tab[(melt.tab}\hlopt{$}\hlstd{gene} \hlopt{%in%} \hlstd{v)}\hlopt{==}\hlnum{FALSE}\hlstd{,]}
\hlkwd{qplot}\hlstd{(}\hlkwc{data}\hlstd{=melt.tab,}
\hlkwc{x}\hlstd{=gene,}
\hlkwc{y}\hlstd{=species,}
\hlkwc{fill}\hlstd{=}\hlkwd{factor}\hlstd{(value),}
\hlkwc{geom}\hlstd{=}\hlstr{"tile"}\hlstd{)}\hlopt{+}
\hlkwd{scale_fill_manual}\hlstd{(}\hlkwc{values}\hlstd{=}\hlkwd{c}\hlstd{(}\hlstr{"0"}\hlstd{=}\hlstr{"white"}\hlstd{,} \hlstr{"1"}\hlstd{=}\hlstr{"red"}\hlstd{))} \hlopt{+}
\hlkwd{theme}\hlstd{(}\hlkwc{axis.text.x} \hlstd{=} \hlkwd{element_text}\hlstd{(}\hlkwc{angle} \hlstd{=} \hlnum{90}\hlstd{))}
\end{alltt}
\end{kframe}
\includegraphics[width=\maxwidth]{figure/heatmap-1}
\end{knitrout}
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.