MRG: fix README code blocks (#54)

* fix README

* fix more

* fix more

* fix more

* fix more

* fix more

* fix more

* fix more

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* upd plots too

README.md

@@ -93,7 +93,7 @@ in format; it must contain at least two columns, one named `category`,
 but can contain more as long as `category` is provided.
 
 The simplest possible categories CSV format is shown in
-[10sketches-categories.csv](examples/10sketches-categories.csv), and
+[10sketches-categories.csv](examples/sketches/10sketches-categories.csv), and
 it contains two columns, `label` and `category`.  When this file is
 loaded, `label` is matched to the name of each point/row/column, and
 that point is then assigned that category.
@@ -122,11 +122,11 @@ Compare 3 sketches with `sourmash compare`, and cluster.
 
 This command:
 ```
-sourmash compare sketches/{2,47,63}.sig.zip -o 3sketches.cmp
+sourmash compare sketches/{2,47,63}.sig.zip -o 3sketches.cmp \
     --labels-to 3sketches.cmp.labels_to.csv
 
 sourmash scripts plot2 3sketches.cmp 3sketches.cmp.labels_to.csv \
-    -o examples/plot2.3sketches.cmp.png
+    -o plot2.3sketches.cmp.png
 ```
 
 produces this plot:
@@ -139,11 +139,11 @@ Compare 3 sketches with `sourmash compare`, cluster, and show a cut point.
 
 This command:
 ```
-sourmash compare sketches/{2,47,63}.sig.zip -o 3sketches.cmp
+sourmash compare sketches/{2,47,63}.sig.zip -o 3sketches.cmp \
     --labels-to 3sketches.cmp.labels_to.csv
 
-sourmash scripts plot2 3sketches.cmp 3sketches.cmp.labels_to_csv \
-    -o examples/plot2.cut.3sketches.cmp.png \
+sourmash scripts plot2 3sketches.cmp 3sketches.cmp.labels_to.csv \
+    -o plot2.cut.3sketches.cmp.png \
     --cut-point=1.2
 ```
 
@@ -180,13 +180,13 @@ Use MDS to display a comparison generated by `sourmash compare`.
 
 These commands:
 ```
-sourmash compare sketches/{2,47,48,49,51,52,53,59,60}.sig.zip \
+sourmash compare sketches/{2,47,48,49,51,52,53,59,60,63}.sig.zip \
     -o 10sketches.cmp \
     --labels-to 10sketches.cmp.labels_to.csv
 
 sourmash scripts mds 10sketches.cmp 10sketches.cmp.labels_to.csv \
     -o mds.10sketches.cmp.png \
-    -C 10sketches-categories.csv
+    -C sketches/10sketches-categories.csv
 ```
 
 produces this plot:
@@ -206,13 +206,13 @@ produces a dense numpy matrix.
 
 These commands:
 ```
-sourmash sig cat sketches/{2,47,48,49,51,52,53,59,60}.sig.zip \
+sourmash sig cat sketches/{2,47,48,49,51,52,53,59,60,63}.sig.zip \
     -o 10sketches.sig.zip
 sourmash scripts pairwise 10sketches.sig.zip -o 10sketches.pairwise.csv
 
-sourmash scripts mds 10sketches.cmp \
-    -o mds.10sketches.cmp.png \
-    -C 10sketches-categories.csv
+sourmash scripts mds2 10sketches.pairwise.csv \
+    -o mds2.10sketches.cmp.png \
+    -C sketches/10sketches-categories.csv
 ```
 
 produces this plot:
@@ -231,7 +231,7 @@ into a categories CSV that can be used to color points and columns/rows.
 These commands:
 ```
 # generate pairwise comparison
-sourmash scripts pairwise 64sketches.sig.zip -o 64sketches.pairwise.csv \
+sourmash scripts pairwise sketches/64sketches.sig.zip -o 64sketches.pairwise.csv \
     --write-all
 
 # generate clusters
@@ -256,7 +256,7 @@ command displays a comparison generated by `sourmash compare`.
 These commands:
 
 ```
-sourmash compare 64sketches.sig.zip -o 64sketches.cmp \
+sourmash compare sketches/64sketches.sig.zip -o 64sketches.cmp \
     --labels-to 64sketches.cmp.labels_to.csv
     
 sourmash scripts tsne 64sketches.cmp 64sketches.cmp.labels_to.csv \
@@ -275,7 +275,7 @@ produce this plot:
 These commands:
 
 ```
-sourmash scripts pairwise 64sketches.sig.zip -o 64sketches.pairwise.csv \
+sourmash scripts pairwise sketches/64sketches.sig.zip -o 64sketches.pairwise.csv \
     --write-all
     
 sourmash scripts tsne2 64sketches.pairwise.csv \
@@ -297,13 +297,13 @@ Convert the sparse comparison CSV (created using the
 These commands:
 ```
 # build pairwise
-sourmash sig cat sketches/{2,47,48,49,51,52,53,59,60}.sig.zip \
+sourmash sig cat sketches/{2,47,48,49,51,52,53,59,60,63}.sig.zip \
     -o 10sketches.sig.zip
 sourmash scripts pairwise 10sketches.sig.zip -o 10sketches.pairwise.csv
 
 # convert pairwise
 sourmash scripts pairwise_to_matrix 10sketches.pairwise.csv \
-    -o 10sketches.pairwise.cmp --write-all \
+    -o 10sketches.pairwise.cmp \
     --labels-to 10sketches.pairwise.cmp.labels_to.csv
     
 # plot!
@@ -324,12 +324,12 @@ offers some nice visualization options.
 
 These commands:
 ```
-sourmash compare sketches/{2,47,48,49,51,52,53,59,60}.sig.zip \
+sourmash compare sketches/{2,47,48,49,51,52,53,59,60,63}.sig.zip \
     -o 10sketches.cmp \
     --labels-to 10sketches.cmp.labels_to.csv
 
 sourmash scripts plot3 10sketches.cmp 10sketches.cmp.labels_to.csv \
-    -o plot3.10sketches.cmp.png -C 10sketches-categories.csv
+    -o plot3.10sketches.cmp.png -C sketches/10sketches-categories.csv
 ```
 
 produce this plot:
@@ -344,15 +344,15 @@ category coloring on rows and columns.
 
 These commands:
 ```
-sourmash sig cat sketches/{2,47,48,49,51,52,53,59,60}.sig.zip \
+sourmash sig cat sketches/{2,47,48,49,51,52,53,59,60,63}.sig.zip \
     -o 10sketches.sig.zip
 
 sourmash scripts manysearch 10sketches.sig.zip \
     sketches/shew21.sig.zip -o 10sketches.manysearch.csv
 
 sourmash scripts clustermap1 10sketches.manysearch.csv \
     -o clustermap1.10sketches.png \
-    -u containment -R 10sketches-categories.csv
+    -u containment -R sketches/10sketches-categories.csv
 ```
 
 produce: