Merge branch 'master' of https://github.com/eead-csic-compbio/get_hom…

…ologues
eead-csic-compbio · Oct 23, 2017 · 3ed63db · 3ed63db
2 parents e40acb2 + efef168
commit 3ed63db
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diff --git a/hcluster_matrix.sh b/hcluster_matrix.sh
@@ -12,7 +12,9 @@
 
 
 progname=${0##*/} 
-VERSION='0.4_7Sep17' # v0.4_7Sep17; added options -x <regex> to select specific rows (genomes) 
+VERSION='0.5_14Oct17' #v'0.5_14Oct17'; added options -A and -X to control the angle 
+                      #                and character eXpansion factor of leaf labels
+         #'0.4_7Sep17' # v0.4_7Sep17; added options -x <regex> to select specific rows (genomes) 
                      #                                       from the input pangenome_matrix_t0.tab
                      #                            -c <0|1> to print or not distances in heatmap cells
 		     #                            -f <int> maximum number of decimals in matrix display (if -c 1)
@@ -42,7 +44,8 @@ function print_help()
     OPTIONAL:
        -a <string> algorithm/method for clustering 
              [ward.D|ward.D2|single|complete|average(=UPGMA)] [def $algorithm]
-       -c <int> 1|0 to display or not the distace values in the heatmap cells [def:$cell_note]
+       -c <int> 1|0 to display or not the distace values      [def:$cell_note]
+                    in the heatmap cells 
        -d <string> distance type [euclidean|manhattan|gower]  [def $distance]
        -f <int> maximum number of decimals in matrix display  [1,2; def:$decimals]
        -t <string> text for Main title                        [def:$text]
@@ -54,14 +57,19 @@ function print_help()
        -W <integer> ouptupt device width                      [def:$width]     
        -N <flag> print Notes and exit                         [flag]
 
-    Select genomes from input pangenome_matrix_t0.tab using regular expressions
+       -A <'integer,integer'> angle to rotate row,col labels  [def $angle]
+       -X <float> leaf label character expansion factor       [def $charExp]
+       
+
+    Select genomes from input pangenome_matrix_t0.tab using regular expressions:
        -x <string> regex, like: 'Escherichia|Salmonella'      [def $regex]
+       
 
     EXAMPLE:
-      $progname -i pangenome_matrix_t0.tab -t "Pan-genome tree for Genus X" -a complete -d manhattan -o pdf -x 'maltoph|genosp' 
+      $progname -i pangenome_matrix_t0.tab -t "Pan-genome tree" -a ward.D2 -d euclidean -o pdf -x 'maltoph|genosp' -A 'NULL,45' -X 0.8
 
     AIM: compute a distance matrix from a pangenome_matrix.tab file produced after running 
-          get_homologues.pl and compare_clusters.pl with options -t 0 -m .
+         get_homologues.pl and compare_clusters.pl with options -t 0 -m .
          The pangenome_matrix.tab file processed by hclust(), and heatmap.2()
     
     OUTPUT: a newick file with extension .ph and svg|pdf output of hclust and heatmap.2 calls
@@ -186,16 +194,22 @@ algorithm=ward.D2
 distance=gower
 decimals=2
 
+charExp=1.0
+angle='NULL,NULL'
+#colTax=1
+
 subset_matrix=0
 
 
 # See bash cookbook 13.1 and 13.2
-while getopts ':a:c:i:d:t:m:o:p:f:v:x:H:W:R:hND?:' OPTIONS
+while getopts ':a:A:c:i:d:t:m:o:p:f:v:x:X:H:W:R:hND?:' OPTIONS
 do
    case $OPTIONS in
 
    a)   algorithm=$OPTARG
         ;;
+   A)   angle=$OPTARG
+        ;;
    c)   cell_note=$OPTARG
         ;;
    d)   distance=$OPTARG
@@ -216,6 +230,8 @@ do
         ;;
    x)   regex=$OPTARG
         ;;
+   X)   charExp=$OPTARG
+        ;;
    C)   reorder_clusters=0
         ;;
    H)   height=$OPTARG
@@ -294,6 +310,7 @@ cat << PARAMS
 	distance:$distance|dist_cutoff:$dist_cutoff|hclustering_meth:$algorithm|cell_note:$cell_note
         text:$text|margin_hor:$margin_hor|margin_vert:$margin_vert|points:$points
         width:$width|height:$height|outformat:$outformat
+	angle:"$angle"|charExp:$charExp
 ##############################################################################################
 
 PARAMS
@@ -307,6 +324,9 @@ tree_file=${tree_file//\//_}
 newick_file="hclust_${distance}-${algorithm}_${tab_file%.*}_tree.ph"
 newick_file=${newick_file//\//_}
 
+aRow=$(echo "$angle" | cut -d, -f1)
+aCol=$(echo "$angle" | cut -d, -f2)
+
 echo ">>> Plotting files $tree_file and $heatmap_outfile ..."
 echo "     this will take some time, please be patient"
 echo
@@ -330,6 +350,8 @@ if($subset_matrix > 0 ){
    table <- table[include_list, ]
 }
 
+
+
 mat_dat <- data.matrix(table[,2:ncol(table)])
 
 rnames <- table[,1]
@@ -348,14 +370,21 @@ dev.off()
     
 if($cell_note == 0){
    $outformat(file="$heatmap_outfile", width=$width, height=$height, pointsize=$pointsize)
-   heatmap.2(as.matrix(my_dist), main="$text $distance dist.", notecol="black", density.info="none", trace="none", dendrogram="row", margins=c($margin_vert,$margin_hor), lhei = c(1,5))
+   heatmap.2(as.matrix(my_dist), main="$text $distance dist.", notecol="black", density.info="none", trace="none", dendrogram="row", 
+   margins=c($margin_vert,$margin_hor), lhei = c(1,5),
+   cexRow=$charExp, cexCol=$charExp, 
+   srtRow=$aRow, srtCol=$aCol)
    dev.off()
 }
 
 if($cell_note == 1){
    $outformat(file="$heatmap_outfile", width=$width, height=$height, pointsize=$pointsize)
-   heatmap.2(as.matrix(my_dist), cellnote=round(as.matrix(my_dist),$decimals), main="$text $distance dist.", notecol="black", density.info="none", trace="none", dendrogram="row",       margins=c($margin_vert,$margin_hor), lhei = c(1,5))
-    dev.off()
+   heatmap.2(as.matrix(my_dist), cellnote=round(as.matrix(my_dist),$decimals), main="$text $distance dist.", 
+   notecol="black", density.info="none", trace="none", dendrogram="row", 
+   margins=c($margin_vert,$margin_hor), lhei = c(1,5),
+   cexRow=$charExp, cexCol=$charExp, 
+   srtRow=$aRow, srtCol=$aCol)
+   dev.off()
 }    
 
 RCMD

diff --git a/plot_matrix_heatmap.sh b/plot_matrix_heatmap.sh
@@ -9,7 +9,8 @@
 #: OUTPUT: svg and pdf; png not implemented yet
 
 progname=${0##*/} # plot_matrix_heatmap.sh
-VERSION='v0.5_18Aug17'   # added options -d (max no. decimals) and -x (filter matrix with regex)
+VERSION='v0.6_14Oct17'   # added options -X (charExp) and -a (label rotation angle)
+         #'v0.5_18Aug17' # added options -d (max no. decimals) and -x (filter matrix with regex)
          #'v0.4_17Aug17' # added option -r to remove column names and cell contents, and -k 
          #'v0.3_13Apr16' # added option -c to filter input matrix by a maximum similarity cut-off value
                          # to reduce excessive redundancy. Improved the help text printed with -M
@@ -41,16 +42,18 @@ function print_help()
        -d <int> maximum number of decimals in matrix display [0-2; def: $decimals]
 	
     II) tweak the graphical output:
-       -t <string> text for plot title                    [def input_tab_file_name]
-       -m <integer> margins_horizontal                    [def $margin_hor]
-       -v <integer> margins_vertical                      [def $margin_vert] 
-       -o <string> output file format                     [def $outformat]
-       -p <integer> points for plotting device            [def $points]    
-       -H <integer> output device height                  [def $height]    
-       -W <integer> output device width                   [def $width]     
-       -C <flag> do not reorder clusters                  [def reorder clusters and plot dendrogram]
-       -r <flag> remove column names and cell contents    [def names and cell contents are printed]
-       -k <string> text for scale X-axis                  [def "Value"]
+       -a <'integer,integer'> angle to rotate row,col labels [def $angle]
+       -t <string> text for plot title                       [def input_tab_file_name]
+       -m <integer> margins_horizontal                       [def $margin_hor]
+       -v <integer> margins_vertical                         [def $margin_vert] 
+       -o <string> output file format                        [def $outformat]
+       -p <integer> points for plotting device               [def $points]    
+       -H <integer> output device height                     [def $height]    
+       -W <integer> output device width                      [def $width]     
+       -C <flag> do not reorder clusters                     [def reorder clusters and plot dendrogram]
+       -r <flag> remove column names and cell contents       [def names and cell contents are printed]
+       -k <string> text for scale X-axis                     [def "Value"]
+       -X <float> character expansion factor                 [def $charExp]
     
     RUN NJ ANALYSIS using ANI matrix (average identity matrix) generated by get_homologues.pl -A -t 0 -M|G
        -N <flag> will compute a distance matrix from the input similarity matrix
@@ -64,7 +67,7 @@ function print_help()
        -M <flag> prints gplot installation instructions and further usage information
        
     EXAMPLE:
-      $progname -i Avg_identity.tab -c 98.5 -t "Genus X ANIb (OMCL all clusters)" -N -o pdf -m 22 -v 22 -p 20 -H 20 -W 30 -x 'Smalt|Smc'
+      $progname -i Avg_identity.tab -c 99.1 -t "ANIb (OMCL core-clusters)" -N -o pdf -m 22 -v 22 -p 20 -H 20 -W 30 -x 'Smalt|Smc' -d 1 -a 'NULL,45' -X 0.9
 
     #------------------------------------------------------------------------------------------------------------------
     AIM: Plot ordered heatmaps with row and col. dendrogram, from squared numeric (distance or presence-absence) matrix,
@@ -179,14 +182,18 @@ reorder_clusters=1
 remove_colnames=0
 key_xaxis="Value"
 decimals=0
+charExp=1.0
+angle='NULL,NULL'
 
 subset_matrix=0
 
 # See bash cookbook 13.1 and 13.2
-while getopts ':c:i:d:t:m:o:p:v:x:H:W:k:hrMNC?:' OPTIONS
+while getopts ':a:c:i:d:t:m:o:p:v:x:X:H:W:k:hrMNC?:' OPTIONS
 do
    case $OPTIONS in
 
+   a)   angle=$OPTARG
+        ;;
    c)   sim_cutoff=$OPTARG
         ;;
    d)   decimals=$OPTARG
@@ -217,6 +224,8 @@ do
         ;;
    x)   regex=$OPTARG
         ;;
+   X)   charExp=$OPTARG
+        ;;
    C)   reorder_clusters=0
         ;;
    \:)   printf "argument missing from -%s option\n" $OPTARG
@@ -270,6 +279,7 @@ cat << PARAMS
         input tab_file = $tab_file | sim_cutoff = $sim_cutoff | max_decimals = $decimals
 	subset_matrix = $subset_matrix | regex = $regex
         text=$text|margin_hor=$margin_hor|margin_vert=$margin_vert|points=$points
+	angle=$angle|charExp=$charExp
         width=$width|height=$height|outformat=$outformat
         reorder_clusters=$reorder_clusters|remove_colnames=$remove_colnames|key_xaxis=$key_xaxis|do_bioNJ=$do_nj
         
@@ -290,6 +300,11 @@ else
    nj_tree="${tab_file%.*}_BioNJ.ph"
 fi
 
+aRow=$(echo "$angle" | cut -d, -f1)
+aCol=$(echo "$angle" | cut -d, -f2)
+
+
+
 # 2) call R using a heredoc and write the resulting script to file 
 R --no-save -q <<RCMD > ${progname%.*}_script_run_at_${start_time}.R
 library("gplots")
@@ -307,12 +322,8 @@ if($subset_matrix > 0 ){
   include_list <- grep("$regex", rownames(mat_dat))
    mat_dat <- mat_dat[include_list, ]
    mat_dat <- mat_dat[,include_list]
-   #mat_dat <- f.mat2
-   #rm(f.mat)
 }
 
-
-
 if($sim_cutoff < 100)
 {
    tmp_mat = mat_dat
@@ -325,26 +336,30 @@ if($reorder_clusters > 0){
   if($remove_colnames > 0){
     $outformat("$heatmap_outfile", width=$width, height=$height, pointsize=$pointsize)  
     heatmap.2(mat_dat, main="$text", notecol="black", density.info="none", key.xlab="$key_xaxis",
-      trace="none", margins=c($margin_vert,$margin_hor), lhei = c(1,5), labCol=F)
+      trace="none", margins=c($margin_vert,$margin_hor), lhei = c(1,5), labCol=F,
+      cexRow=$charExp, cexCol=$charExp, srtRow=$aRow, srtCol=$aCol)
     dev.off()
   }
   else {
     $outformat("$heatmap_outfile", width=$width, height=$height, pointsize=$pointsize)  
     heatmap.2(mat_dat, cellnote=mat_dat, main="$text", notecol="black", density.info="none", key.xlab="$key_xaxis",
-      trace="none", margins=c($margin_vert,$margin_hor), lhei = c(1,5))
+      trace="none", margins=c($margin_vert,$margin_hor), lhei = c(1,5), 
+      cexRow=$charExp, cexCol=$charExp, srtRow=$aRow, srtCol=$aCol)
     dev.off()
   }
 } else {
   if($remove_colnames > 0){
     $outformat("$heatmap_outfile", width=$width, height=$height, pointsize=$pointsize)  
     heatmap.2(mat_dat, main="$text", notecol="black", density.info="none", labCol=F, key.xlab="$key_xaxis",
-    trace="none", margins=c($margin_vert,$margin_hor), lhei = c(1,5), dendrogram = "row", Colv = FALSE)
+    trace="none", margins=c($margin_vert,$margin_hor), lhei = c(1,5), dendrogram = "row", Colv = FALSE, 
+    cexRow=$charExp, cexCol=$charExp, srtRow=$aRow, srtCol=$aCol)
     dev.off()
   }
   else {
     $outformat("$heatmap_outfile", width=$width, height=$height, pointsize=$pointsize)  
     heatmap.2(mat_dat, cellnote=mat_dat, main="$text", notecol="black", density.info="none", key.xlab="$key_xaxis",
-    trace="none", margins=c($margin_vert,$margin_hor), lhei = c(1,5), dendrogram = "row", Colv = FALSE)
+    trace="none", margins=c($margin_vert,$margin_hor), lhei = c(1,5), dendrogram = "row", Colv = FALSE,
+    cexRow=$charExp, cexCol=$charExp, srtRow=$aRow, srtCol=$aCol)
     dev.off()
   }
 }