Small coding updates, exemplary code, spacing of PDF slides.

Author: V-Z

presentation/hybseq_course.tex

@@ -67,10 +67,10 @@
 	}
 
 % Fixing space before and after block of code higlight
-\BeforeBeginEnvironment{bashcode}{\vspace{-0.5em}}
-\AfterEndEnvironment{bashcode}{\par\vspace{-0.5em}}
-\BeforeBeginEnvironment{spluscode}{\vspace{-0.5em}}
-\AfterEndEnvironment{spluscode}{\par\vspace{-0.5em}}
+\BeforeBeginEnvironment{bashcode}{\vspace{-0.25em}}
+\AfterEndEnvironment{bashcode}{\par\vspace{-0.25em}}
+\BeforeBeginEnvironment{spluscode}{\vspace{-0.25em}}
+\AfterEndEnvironment{spluscode}{\par\vspace{-0.25em}}
 
 % % Fixing space before and after multicols region
 % \BeforeBeginEnvironment{multicols}{\vspace{-0.5em}}
@@ -381,7 +381,7 @@ \subsection{General data structure}
         I       ├── Assembly_1 # Gene output directory
         I       ├── ... # More gene output directories...
         I       └── Assembly_16358 # Gene output directory...
-        I    # Plenty of reconstructed contigs, statistics, etc.
+        I   ... # Plenty of reconstructed contigs, statistics, etc.
         ├── 3_aligned # Aligned contigs
         I   ├── exons # Aligned exons
         I   ├── introns # Aligned introns
@@ -429,6 +429,7 @@ \subsection{Data download and start}
     wget https://botany.natur.cuni.cz/zeisek/hybseq_course_zingibers_0_data.zip
     # Unpack it
     unzip hybseq_course_zingibers_0_data.zip
+    ls -lha hybseq_course_zingibers/ # See it
 	\end{bashcode}
 	\begin{itemize}
 		 \item The archive contains input raw data and reference
@@ -977,13 +978,16 @@ \subsection{Post-processing gene trees}
 	\end{itemize}
 	\begin{bashcode}
     # Move qsub logs to the 'trees' directory
-    cd ~/hybseq_course_zingibers/3_aligned/ && mv HybSeq.genetree.* trees/
+    cd ~/hybseq_course_zingibers/3_aligned/ # Ensure to be in 3_aligned
+    mv HybSeq.genetree.* trees/ # Move...
     # Everything should be moved from XXX/2_seqs/aligned to XXX/3_aligned
-    mv trees ../4_gene_trees && cd ../
+    mv trees ../4_gene_trees
+    cd ../ && ls -lha
     # Post-process (sort into subdirectories and get lists of gene trees)
     # all gene trees - provide path to directory with gene trees files
     ~/hybseq/bin/hybseq_5_gene_trees_4_postprocess.sh 4_gene_trees | tee \
       hybseq_gene_trees_postprocess.log
+    mv hybseq_gene_trees_postprocess.log 4_gene_trees/ && ls -lha 4_gene_trees/
 	\end{bashcode}
 	\begin{itemize}
 		\item Wait for tasks to finish, or \href{https://botany.natur.cuni.cz/zeisek/hybseq_course_zingibers_4_gene_trees.zip}{download} and inspect test data
@@ -1029,7 +1033,7 @@ \section{Comparing gene trees}
 \begin{frame}[fragile]{Install needed R packages}
 	\begin{itemize}
 		\item The tasks will be done in \href{https://www.r-project.org/}{R} (use e.g. \href{https://posit.co/products/open-source/rstudio/}{RStudio} or \href{https://rkward.kde.org/}{RKWard})
-		\item Use your notebook or e.g. MetaCentrum \href{https://docs.metacentrum.cz/software/ondemand/}{OnDemand} RStudio or \href{https://docs.metacentrum.cz/related/jupyter/}{Jupyter notebook}
+		\item Use your notebook or e.g. MetaCentrum \href{https://docs.metacentrum.cz/en/docs/ondemand}{OnDemand} RStudio or \href{https://docs.metacentrum.cz/en/docs/related/jupyter}{Jupyter notebook}
 		\item Following R code is available at \url{https://github.com/V-Z/hybseq-course/blob/master/trees_filtration.r} --- \alert{\textbf{download} it and edit} according to your needs
 	\end{itemize}
 	\begin{spluscode}
@@ -1170,7 +1174,7 @@ \subsection{Filtering trees}
 	\begin{spluscode}
     trees # See original trees
     # Remove trees identified in the PCoA plot
-    trees[c("Assembly_1033", "Assembly_10103", "Assembly_10222")] <- NULL
+    trees[c("Assembly_1033", "Assembly_13627", "Assembly_15852")] <- NULL
     trees # See new object
     # Possibly remove trees with too few tips
     print(trees, details=TRUE)
@@ -1536,7 +1540,7 @@ \subsection{Comparing trees}
     # Pie chart: concordance (blue) top conflict (green), other conflict
     # (red), no signal (gray). Run phypartspiecharts.py to get the graphics:
     python phypartspiecharts.py --svg_name trees_good_res.svg \
-      parsimony_sp_tree.nwk trees_good_res 20
+      parsimony_sp_tree.nwk trees_good_res 221
 	\end{bashcode}
 \end{frame}
 

presentation/pcoa.png

@@ -49,7 +49,7 @@ title("PCoA of matrix of pairwise trees distances")
 
 # Remove outlying trees
 trees
-trees[c("Assembly_1033", "Assembly_10103", "Assembly_10222")] <- NULL
+trees[c("Assembly_1033", "Assembly_13627", "Assembly_15852")] <- NULL
 trees
 
 # Now you can repeat recalculation of distance matrix and PCoA and possibly remove more trees...
@@ -111,12 +111,12 @@ plot.phylo(x = tree.sp2, type = "phylogram", edge.width = 2, label.offset = 0.01
 
 # # Consensus networks
 # # Requires all trees to have same set of tips (no missing data)
-# # ?consensusNet
+# ?consensusNet
 # # Compute consensus network
-# # tree.net <- consensusNet(obj = trees.good, prob = 0.25)
+# tree.net <- consensusNet(obj = trees.good, prob = 0.25)
 # # Plot 2D or 3D
-# # plot(x = tree.net, planar = FALSE, type = "2D", use.edge.length = TRUE, show.tip.label = TRUE, show.edge.label = TRUE, show.node.label = TRUE, show.nodes = TRUE, edge.color = "black", tip.color = "blue") # 2D
-# # plot(x = tree.net, planar = FALSE, type = "3D", use.edge.length = TRUE, show.tip.label = TRUE, show.edge.label = TRUE, show.node.label = TRUE, show.nodes = TRUE, edge.color = "black", tip.color = "blue") # 3D
+# plot(x = tree.net, planar = FALSE, type = "2D", use.edge.length = TRUE, show.tip.label = TRUE, show.edge.label = TRUE, show.node.label = TRUE, show.nodes = TRUE, edge.color = "black", tip.color = "blue") # 2D
+# plot(x = tree.net, planar = FALSE, type = "3D", use.edge.length = TRUE, show.tip.label = TRUE, show.edge.label = TRUE, show.node.label = TRUE, show.nodes = TRUE, edge.color = "black", tip.color = "blue") # 3D
 
 # Save trees.good in NEXUS for PhyloNet
 write.nexus(trees.good, file = "trees_good.nex", translate = FALSE)
@@ -146,6 +146,6 @@ densiTree(x = trees.ultra[1:10], scaleX = TRUE, width = 5, cex = 1.25)
 ?phytools::densityTree
 # Plotting density trees
 densityTree(trees = c(tree.sp, tree.sp2), fix.depth = TRUE, lwd = 4)
-densityTree(trees = trees.ultra, fix.depth = TRUE, use.gradient = TRUE, alpha = 0.5, lwd = 4)
+# densityTree(trees = trees.ultra, fix.depth = TRUE, use.gradient = TRUE, alpha = 0.5, lwd = 4)
 # densityTree(trees = trees.ultra[1:3], fix.depth = TRUE, use.gradient = TRUE, alpha = 0.5, lwd = 4)
 # densityTree(trees = trees.ultra[c(2, 4, 6)], fix.depth = TRUE, use.gradient = TRUE, alpha = 0.5, lwd = 4)