diff --git a/doc/1_reference_legio_phylo.Rnw b/doc/1_reference_legio_phylo.Rnw
index c8907eb193c6c47b68feae50600ec2e89e2f3ad1..79e1d0c55c148b5a58382c673ace11cd75b5dcd5 100644
--- a/doc/1_reference_legio_phylo.Rnw
+++ b/doc/1_reference_legio_phylo.Rnw
@@ -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}
diff --git a/doc/1_reference_legio_phylo.aux b/doc/1_reference_legio_phylo.aux
index 16fa2758ad7b946bc505e87cffafad514759911b..f797f33112eaa2059bc8d094ce5798862b0d719a 100644
--- a/doc/1_reference_legio_phylo.aux
+++ b/doc/1_reference_legio_phylo.aux
@@ -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}}
diff --git a/doc/1_reference_legio_phylo.log b/doc/1_reference_legio_phylo.log
index 78c41e7d2344f44406333f6c021fc2e226591504..88097df49479062fdcf1c680bc9fdecade07bc1f 100644
--- a/doc/1_reference_legio_phylo.log
+++ b/doc/1_reference_legio_phylo.log
@@ -1,4 +1,4 @@
-This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex 2021.6.16) 25 JAN 2022 10:21
+This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex 2021.6.16) 25 JAN 2022 11:58
entering extended mode
restricted \write18 enabled.
%&-line parsing enabled.
@@ -833,45 +833,45 @@ n\OT1/cmtt/m/n/10.95 t"[][],[] []fill[][]=[][]TRUE[][],[] []header[][]=[][]TRUE
[]
-Overfull \hbox (272.35565pt too wide) in paragraph at lines 158--158
+Overfull \hbox (352.83728pt too wide) in paragraph at lines 158--158
[]\OT1/cmtt/m/n/10.95 ## Species ATCC.number Strain.designation
- Isolation ORF.prefix[]
+ Isolation ORF.prefix Accession[]
[]
-Overfull \hbox (272.35565pt too wide) in paragraph at lines 158--158
+Overfull \hbox (352.83728pt too wide) in paragraph at lines 158--158
[]\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[]
[]
-Overfull \hbox (272.35565pt too wide) in paragraph at lines 158--158
+Overfull \hbox (352.83728pt too wide) in paragraph at lines 158--158
[]\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 []
[]
-Overfull \hbox (272.35565pt too wide) in paragraph at lines 158--158
+Overfull \hbox (352.83728pt too wide) in paragraph at lines 158--158
[]\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 []
[]
-Overfull \hbox (272.35565pt too wide) in paragraph at lines 158--158
+Overfull \hbox (352.83728pt too wide) in paragraph at lines 158--158
[]\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 []
[]
-Overfull \hbox (272.35565pt too wide) in paragraph at lines 158--158
+Overfull \hbox (352.83728pt too wide) in paragraph at lines 158--158
[]\OT1/cmtt/m/n/10.95 ## 5 L. brunensis ATCC43878 ATCC43878
- Cooling tower water (Czechoslovakia) Lbru[]
+ Cooling tower water (Czechoslovakia) Lbru LNXV00000000 []
[]
-Overfull \hbox (272.35565pt too wide) in paragraph at lines 158--158
+Overfull \hbox (352.83728pt too wide) in paragraph at lines 158--158
[]\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[]
[]
-Overfull \hbox (197.62271pt too wide) in paragraph at lines 310--310
+Overfull \hbox (312.59647pt too wide) in paragraph at lines 310--310
[]\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[]
[]
-Overfull \hbox (197.62271pt too wide) in paragraph at lines 337--337
+Overfull \hbox (312.59647pt too wide) in paragraph at lines 337--337
[]\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[]
[]
-Overfull \hbox (197.62271pt too wide) in paragraph at lines 377--377
+Overfull \hbox (312.59647pt too wide) in paragraph at lines 377--377
[]\OT1/cmtt/m/n/10.95 ## 73 Levels: Aquicella lusitana Aquicella siphonis Burkh
-olderia cepacia ... Rickettsiella grylli[]
+olderia cepacia Burkholderia mallei ... Rickettsiella grylli[]
[]
@@ -2022,132 +2022,120 @@ OR+lpg2330+OR+lpg1767+OR+lpg231--.tab.gz"[]
Package xcolor Warning: Incompatible color definition on input line 636.
[12]
-Overfull \hbox (266.60696pt too wide) in paragraph at lines 659--659
+Overfull \hbox (364.33466pt too wide) in paragraph at lines 657--657
[]\OT1/cmtt/m/n/10.95 ## [1] "Q5ZRF4_lpg2928" "Q5ZRP4_lpg2836" "Q5ZRQ7_lpg2823
-" "Q5ZRT6_lpg2792" "Q5ZRV3_lpg2773" "Q5ZRV4_lpg2772"[]
+" "Q5ZRT6_lpg2792" "Q5ZRV3_lpg2773" "Q5ZRV4_lpg2772" "Q5ZRV6_lpg2770"[]
[]
-Overfull \hbox (266.60696pt too wide) in paragraph at lines 659--659
-[]\OT1/cmtt/m/n/10.95 ## [7] "Q5ZRV6_lpg2770" "Q5ZRW1_lpg2765" "Q5ZRX2_lpg2754
-" "Q5ZRZ3_lpg2727" "Q5ZS05_lpg2714" "Q5ZS08_lpg2711"[]
+Overfull \hbox (364.33466pt too wide) in paragraph at lines 657--657
+[]\OT1/cmtt/m/n/10.95 ## [8] "Q5ZRW1_lpg2765" "Q5ZRX2_lpg2754" "Q5ZRZ3_lpg2727
+" "Q5ZS05_lpg2714" "Q5ZS08_lpg2711" "Q5ZS49_lpg2670" "Q5ZS63_lpg2656"[]
[]
-Overfull \hbox (266.60696pt too wide) in paragraph at lines 659--659
-[]\OT1/cmtt/m/n/10.95 ## [13] "Q5ZS49_lpg2670" "Q5ZS63_lpg2656" "Q5ZS65_lpg2654
-" "Q5ZT28_lpg2337" "Q5ZT35_lpg2330" "Q5ZT51_lpg2314"[]
+Overfull \hbox (364.33466pt too wide) in paragraph at lines 657--657
+[]\OT1/cmtt/m/n/10.95 ## [15] "Q5ZS65_lpg2654" "Q5ZT28_lpg2337" "Q5ZT35_lpg2330
+" "Q5ZT51_lpg2314" "Q5ZT61_lpg2304" "Q5ZT63_lpg2302" "Q5ZTX1_lpg2037"[]
[]
-Overfull \hbox (266.60696pt too wide) in paragraph at lines 659--659
-[]\OT1/cmtt/m/n/10.95 ## [19] "Q5ZT61_lpg2304" "Q5ZT63_lpg2302" "Q5ZTX1_lpg2037
-" "Q5ZTX7_lpg2031" "Q5ZU05_lpg2003" "Q5ZU96_lpg1911"[]
+Overfull \hbox (364.33466pt too wide) in paragraph at lines 657--657
+[]\OT1/cmtt/m/n/10.95 ## [22] "Q5ZTX7_lpg2031" "Q5ZU05_lpg2003" "Q5ZU96_lpg1911
+" "Q5ZUH7_lpg1821" "Q5ZUJ7_lpg1801" "Q5ZUM6_lpg1767" "Q5ZUS0_lpg1722"[]
[]
-Overfull \hbox (266.60696pt too wide) in paragraph at lines 659--659
-[]\OT1/cmtt/m/n/10.95 ## [25] "Q5ZUH7_lpg1821" "Q5ZUJ7_lpg1801" "Q5ZUM6_lpg1767
-" "Q5ZUS0_lpg1722" "Q5ZUS8_lpg1714" "Q5ZUT0_lpg1712"[]
+Overfull \hbox (364.33466pt too wide) in paragraph at lines 657--657
+[]\OT1/cmtt/m/n/10.95 ## [29] "Q5ZUS8_lpg1714" "Q5ZUT0_lpg1712" "Q5ZVH3_lpg1467
+" "Q5ZVJ6_lpg1444" "Q5ZVJ7_lpg1443" "Q5ZVL5_lpg1425" "Q5ZVP0_lpg1400"[]
[]
-Overfull \hbox (266.60696pt too wide) in paragraph at lines 659--659
-[]\OT1/cmtt/m/n/10.95 ## [31] "Q5ZVH3_lpg1467" "Q5ZVJ6_lpg1444" "Q5ZVJ7_lpg1443
-" "Q5ZVL5_lpg1425" "Q5ZVP0_lpg1400" "Q5ZVP1_lpg1399"[]
+Overfull \hbox (364.33466pt too wide) in paragraph at lines 657--657
+[]\OT1/cmtt/m/n/10.95 ## [36] "Q5ZVP1_lpg1399" "Q5ZVU2_lpg1348" "Q5ZVV6_lpg1334
+" "Q5ZVY2_lpg1306" "Q5ZWA4_lpg1181" "Q5ZWZ6_lpg0937" "Q5ZXE5_lpg0786"[]
[]
-Overfull \hbox (266.60696pt too wide) in paragraph at lines 659--659
-[]\OT1/cmtt/m/n/10.95 ## [37] "Q5ZVU2_lpg1348" "Q5ZVV6_lpg1334" "Q5ZVY2_lpg1306
-" "Q5ZWA4_lpg1181" "Q5ZWZ6_lpg0937" "Q5ZXE5_lpg0786"[]
- []
-
-
-Overfull \hbox (266.60696pt too wide) in paragraph at lines 659--659
+Overfull \hbox (364.33466pt too wide) in paragraph at lines 657--657
[]\OT1/cmtt/m/n/10.95 ## [43] "Q5ZXJ7_lpg0734" "Q5ZXK6_lpg0725" "Q5ZXL2_lpg0719
-" "Q5ZXN3_lpg0698" "Q5ZXP3_lpg0688" "Q5ZXP6_lpg0685"[]
- []
-
-
-Overfull \hbox (266.60696pt too wide) in paragraph at lines 659--659
-[]\OT1/cmtt/m/n/10.95 ## [49] "Q5ZXZ2_lpg0588" "Q5ZY30_lpg0543" "Q5ZY59_lpg0513
-" "Q5ZY67_lpg0505" "Q5ZY69_lpg0503" "Q5ZYH2_lpg0400"[]
+" "Q5ZXN3_lpg0698" "Q5ZXP3_lpg0688" "Q5ZXP6_lpg0685" "Q5ZXZ2_lpg0588"[]
[]
-Overfull \hbox (266.60696pt too wide) in paragraph at lines 659--659
-[]\OT1/cmtt/m/n/10.95 ## [55] "Q5ZYL9_lpg0353" "Q5ZYM1_lpg0351" "Q5ZYM4_lpg0348
-" "Q5ZYM6_lpg0346" "Q5ZYM7_lpg0345" "Q5ZYM8_lpg0344"[]
+Overfull \hbox (364.33466pt too wide) in paragraph at lines 657--657
+[]\OT1/cmtt/m/n/10.95 ## [50] "Q5ZY30_lpg0543" "Q5ZY59_lpg0513" "Q5ZY67_lpg0505
+" "Q5ZY69_lpg0503" "Q5ZYH2_lpg0400" "Q5ZYL9_lpg0353" "Q5ZYM1_lpg0351"[]
[]
-Overfull \hbox (266.60696pt too wide) in paragraph at lines 659--659
-[]\OT1/cmtt/m/n/10.95 ## [61] "Q5ZYM9_lpg0343" "Q5ZYN1_lpg0341" "Q5ZYN4_lpg0338
-" "Q5ZYN6_lpg0336" "Q5ZYN7_lpg0335" "Q5ZYN8_lpg0334"[]
+Overfull \hbox (364.33466pt too wide) in paragraph at lines 657--657
+[]\OT1/cmtt/m/n/10.95 ## [57] "Q5ZYM4_lpg0348" "Q5ZYM6_lpg0346" "Q5ZYM7_lpg0345
+" "Q5ZYM8_lpg0344" "Q5ZYM9_lpg0343" "Q5ZYN1_lpg0341" "Q5ZYN4_lpg0338"[]
[]
-Overfull \hbox (266.60696pt too wide) in paragraph at lines 659--659
-[]\OT1/cmtt/m/n/10.95 ## [67] "Q5ZYP0_lpg0332" "Q5ZYP1_lpg0331" "Q5ZYP2_lpg0330
-" "Q5ZYP3_lpg0329" "Q5ZYP4_lpg0328" "Q5ZYP7_lpg0325"[]
+Overfull \hbox (364.33466pt too wide) in paragraph at lines 657--657
+[]\OT1/cmtt/m/n/10.95 ## [64] "Q5ZYN6_lpg0336" "Q5ZYN7_lpg0335" "Q5ZYN8_lpg0334
+" "Q5ZYP0_lpg0332" "Q5ZYP1_lpg0331" "Q5ZYP2_lpg0330" "Q5ZYP3_lpg0329"[]
[]
-Overfull \hbox (168.87927pt too wide) in paragraph at lines 659--659
-[]\OT1/cmtt/m/n/10.95 ## [73] "Q5ZYQ0_lpg0322" "Q5ZYQ3_lpg0319" "Q5ZYQ4_lpg0318
-" "Q5ZYQ5_lpg0317" "Q5ZYS4_lpg0287"[]
+Overfull \hbox (364.33466pt too wide) in paragraph at lines 657--657
+[]\OT1/cmtt/m/n/10.95 ## [71] "Q5ZYP4_lpg0328" "Q5ZYP7_lpg0325" "Q5ZYQ0_lpg0322
+" "Q5ZYQ3_lpg0319" "Q5ZYQ4_lpg0318" "Q5ZYQ5_lpg0317" "Q5ZYS4_lpg0287"[]
[]
-Overfull \hbox (220.61746pt too wide) in paragraph at lines 672--672
+Overfull \hbox (220.61746pt too wide) in paragraph at lines 670--670
[] []\OT1/cmtt/m/n/10.95 fasta[][]<-[][]read.dna[][]([][]paste0[][](aln,
[] []"/"[][],subrepcurrent,[] []"/"[][], file),[] []format[][]=[][]"fasta"[][],
[] []as.character[][]=[][]TRUE[][])[][]
[]
-Overfull \hbox (48.15683pt too wide) in paragraph at lines 673--673
+Overfull \hbox (48.15683pt too wide) in paragraph at lines 671--671
[] []\OT1/cmtt/m/n/10.95 tmprownames[][]<-[][]ifelse[][]([][]grepl[][]([
][]rownames[][](fasta),[] []pattern[] []=[] []"pneumo"[][]),[][]
[]
-Overfull \hbox (151.63321pt too wide) in paragraph at lines 674--674
+Overfull \hbox (151.63321pt too wide) in paragraph at lines 672--672
[] []\OT1/cmtt/m/n/10.95 substr[][]([][]rownames[][](fasta)[[][]grep
[][]([][]pattern[] []=[] []"pneumophila"[][],[][]rownames[][](fasta))],[] []1[]
[],[][]31[][]),[][]
[]
-Overfull \hbox (168.87927pt too wide) in paragraph at lines 675--675
+Overfull \hbox (168.87927pt too wide) in paragraph at lines 673--673
[] []\OT1/cmtt/m/n/10.95 sapply[][]([][]rownames[][](fasta),[] []fun
ction[][]([][]x[][])[] []strsplit[][](x,[] []split[][]=[][]"."[][],[] []fixed[]
[]=[][]TRUE[][])[[[][]1[][]]][[][]1[][]]))[][]
[]
-Overfull \hbox (220.61746pt too wide) in paragraph at lines 775--775
+Overfull \hbox (220.61746pt too wide) in paragraph at lines 773--773
[] []\OT1/cmtt/m/n/10.95 fasta[][]<-[][]read.dna[][]([][]paste0[][](aln,
[] []"/"[][],subrepcurrent,[] []"/"[][], file),[] []format[][]=[][]"fasta"[][],
[] []as.character[][]=[][]TRUE[][])[][]
[]
-Overfull \hbox (48.15683pt too wide) in paragraph at lines 777--777
+Overfull \hbox (48.15683pt too wide) in paragraph at lines 775--775
[] []\OT1/cmtt/m/n/10.95 tmprownames[][]<-[][]ifelse[][]([][]grepl[][]([
][]rownames[][](fasta),[] []pattern[] []=[] []"pneumo"[][]),[][]
[]
-Overfull \hbox (128.63846pt too wide) in paragraph at lines 778--778
+Overfull \hbox (128.63846pt too wide) in paragraph at lines 776--776
[] []\OT1/cmtt/m/n/10.95 substr[][]([][]rownames[][](fasta)[[][]grep[][]
([][]pattern[] []=[] []"pneumophila"[][],[][]rownames[][](fasta))],[] []1[][],[
][]31[][]),[][]
[]
-Overfull \hbox (145.88452pt too wide) in paragraph at lines 779--779
+Overfull \hbox (145.88452pt too wide) in paragraph at lines 777--777
[] []\OT1/cmtt/m/n/10.95 sapply[][]([][]rownames[][](fasta),[] []functio
n[][]([][]x[][])[] []strsplit[][](x,[] []split[][]=[][]"."[][],[] []fixed[][]=[
][]TRUE[][])[[[][]1[][]]][[][]1[][]]))[][]
@@ -2220,25 +2208,66 @@ Overfull \hbox (17.0pt too wide) in paragraph at lines 826--828
[][]
[]
-Package atveryend Info: Empty hook `BeforeClearDocument' on input line 829.
+
+Package xcolor Warning: Incompatible color definition on input line 830.
+
[20]
Overfull \vbox (89.34718pt too high) has occurred while \output is active []
[21 <./figure/tree-1.pdf>]
-Package atveryend Info: Empty hook `AfterLastShipout' on input line 829.
+Overfull \hbox (151.63321pt too wide) in paragraph at lines 835--835
+[][]\OT1/cmtt/m/n/10.95 dat[] []<-[] []data.frame[][]([][]weather[][]=[][]c[][]
+([][]"Rain"[][],[][]"Hail"[][],[][]"Sunny"[][]),[] []Germany[] []=[] []c[][]([]
+[]0[][],[][]1[][],[][]0[][]),[] []Italy[] []=[] []c[][]([][]1[][],[][]0[][],[][
+]0[][]))[][]
+ []
+
+
+Overfull \hbox (7.91602pt too wide) in paragraph at lines 837--837
+[][]\OT1/cmtt/m/n/10.95 melt.data[][]<-[][]melt[][](dat,[] []id.vars[][]=[][]"w
+eather"[][],[] []variable_name[][]=[][]"country"[][])[][]
+ []
+
+<figure/heatmap-1.pdf, id=186, 650.43pt x 867.24pt>
+File: figure/heatmap-1.pdf Graphic file (type pdf)
+<use figure/heatmap-1.pdf>
+Package pdftex.def Info: figure/heatmap-1.pdf used on input line 867.
+(pdftex.def) Requested size: 360.0pt x 480.01384pt.
+
+Package xcolor Warning: Incompatible color definition on input line 870.
+
+
+Overfull \hbox (17.0pt too wide) in paragraph at lines 867--870
+[][]
+ []
+
+[22] [23 <./figure/heatmap-1.pdf>]
+<figure/heatmap2-1.pdf, id=200, 650.43pt x 867.24pt>
+File: figure/heatmap2-1.pdf Graphic file (type pdf)
+<use figure/heatmap2-1.pdf>
+Package pdftex.def Info: figure/heatmap2-1.pdf used on input line 881.
+(pdftex.def) Requested size: 360.0pt x 480.01384pt.
+
+Overfull \hbox (17.0pt too wide) in paragraph at lines 881--883
+[][]
+ []
+
+Package atveryend Info: Empty hook `BeforeClearDocument' on input line 884.
+[24] [25 <./figure/heatmap2-1.pdf>]
+Package atveryend Info: Empty hook `AfterLastShipout' on input line 884.
(./1_reference_legio_phylo.aux)
-Package atveryend Info: Executing hook `AtVeryEndDocument' on input line 829.
-Package atveryend Info: Executing hook `AtEndAfterFileList' on input line 829.
+Package atveryend Info: Executing hook `AtVeryEndDocument' on input line 884.
+Package atveryend Info: Executing hook `AtEndAfterFileList' on input line 884.
Package rerunfilecheck Info: File `1_reference_legio_phylo.out' has not changed
.
-(rerunfilecheck) Checksum: 5074378731678E119ABCEDC6880C063F;843.
-Package atveryend Info: Empty hook `AtVeryVeryEnd' on input line 829.
+(rerunfilecheck) Checksum: 5928BF33B0DDA372070BC00E8A485420;829.
+Package atveryend Info: Empty hook `AtVeryVeryEnd' on input line 884.
)
Here is how much of TeX's memory you used:
- 7843 strings out of 492982
- 112338 string characters out of 6134896
- 217412 words of memory out of 5000000
- 11287 multiletter control sequences out of 15000+600000
+ 7857 strings out of 492982
+ 112643 string characters out of 6134896
+ 217901 words of memory out of 5000000
+ 11295 multiletter control sequences out of 15000+600000
9834 words of font info for 35 fonts, out of 8000000 for 9000
1141 hyphenation exceptions out of 8191
28i,6n,35p,442b,373s stack positions out of 5000i,500n,10000p,200000b,80000s
@@ -2252,10 +2281,10 @@ c/amsfonts/cm/cmr17.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfo
nts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm
/cmti10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt1
0.pfb></usr/share/texmf/fonts/type1/public/cm-super/sfrm1095.pfb>
-Output written on 1_reference_legio_phylo.pdf (21 pages, 179101 bytes).
+Output written on 1_reference_legio_phylo.pdf (25 pages, 237833 bytes).
PDF statistics:
- 229 PDF objects out of 1000 (max. 8388607)
- 188 compressed objects within 2 object streams
- 35 named destinations out of 1000 (max. 500000)
- 112 words of extra memory for PDF output out of 10000 (max. 10000000)
+ 262 PDF objects out of 1000 (max. 8388607)
+ 212 compressed objects within 3 object streams
+ 39 named destinations out of 1000 (max. 500000)
+ 122 words of extra memory for PDF output out of 10000 (max. 10000000)
diff --git a/doc/1_reference_legio_phylo.out b/doc/1_reference_legio_phylo.out
index 812488015cc6549c9faaa84a3cad0527e26a834a..7ad4583fe5a7f19b3875845dc49cb197f76c5099 100644
--- a/doc/1_reference_legio_phylo.out
+++ b/doc/1_reference_legio_phylo.out
@@ -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
diff --git a/doc/1_reference_legio_phylo.pdf b/doc/1_reference_legio_phylo.pdf
index e7ccefddc522613c2affb660c2fcefff61386c6e..c9cf61206a3409598cf17ffa4a62c06e4b726875 100644
Binary files a/doc/1_reference_legio_phylo.pdf and b/doc/1_reference_legio_phylo.pdf differ
diff --git a/doc/1_reference_legio_phylo.tex b/doc/1_reference_legio_phylo.tex
index 047c198051da11d6d5f76877d188d53834dd3f65..a58464617ad3690a03eaec323180a347a54212c4 100644
--- a/doc/1_reference_legio_phylo.tex
+++ b/doc/1_reference_legio_phylo.tex
@@ -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, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlkwd{qplot}\hlstd{(}\hlkwc{data}\hlstd{=melt.tab,}
+ \hlkwc{x}\hlstd{=species,}
+ \hlkwc{y}\hlstd{=gene,}
+ \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/heatmap2-1}
+\end{knitrout}
+
\end{document}
diff --git a/doc/1_reference_legio_phylo.toc b/doc/1_reference_legio_phylo.toc
index 8d6b229d571384426462159c68e9e9f4dd52e108..7b7cb9e5f03806ec53833357c71a4873bb2155dc 100644
--- a/doc/1_reference_legio_phylo.toc
+++ b/doc/1_reference_legio_phylo.toc
@@ -9,4 +9,4 @@
\contentsline {subsection}{\numberline {2.1}Get sequences from Burstein et al.}{12}{subsection.2.1}
\contentsline {section}{\numberline {3}Phylogeny}{13}{section.3}
\contentsline {subsection}{\numberline {3.1}Genes alignement}{13}{subsection.3.1}
-\contentsline {subsection}{\numberline {3.2}Concatenate and Supertree}{20}{subsection.3.2}
+\contentsline {subsection}{\numberline {3.2}Concatenate}{20}{subsection.3.2}
diff --git a/doc/figure/barplot1-1.pdf b/doc/figure/barplot1-1.pdf
index a65db9c6d3bf74bd04e51e4485322237791085de..535108e904c1f8c32b1c9d4d2e048c2f6700f21c 100644
Binary files a/doc/figure/barplot1-1.pdf and b/doc/figure/barplot1-1.pdf differ
diff --git a/doc/figure/barplot2-1.pdf b/doc/figure/barplot2-1.pdf
index 116e2325df3f91294dc3d2eb257d9112c3c7cb97..f3926c0cd4c4446991c7b4541c37dc70dc15a79c 100644
Binary files a/doc/figure/barplot2-1.pdf and b/doc/figure/barplot2-1.pdf differ
diff --git a/doc/figure/heatmap-1.pdf b/doc/figure/heatmap-1.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..49ea071ac196630e22bdbf915d1a726e5faf15b5
Binary files /dev/null and b/doc/figure/heatmap-1.pdf differ
diff --git a/doc/figure/heatmap2-1.pdf b/doc/figure/heatmap2-1.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..8fb742b85671b00670d06c67574a7837b578d34c
Binary files /dev/null and b/doc/figure/heatmap2-1.pdf differ
diff --git a/doc/figure/tree-1.pdf b/doc/figure/tree-1.pdf
index 3ac19479d557572bb3576b65a6a00e682505cc4a..e3c666b0ed5485e2d71e499cd60a2213d797f80b 100644
Binary files a/doc/figure/tree-1.pdf and b/doc/figure/tree-1.pdf differ