Png2pgv

R/gGnome.R

@@ -5824,7 +5824,8 @@ gGraph = R6::R6Class("gGraph",
                            ## remove zero or NA weight loose ends
                            loose.ed = loose.ed[!is.na(weight), ][weight>0, ]
                            ## add cid values for loose ends
-                           loose.ed[, (cid.field) := 1:.N + nrow(ed)]
+                           max.cid = max(ed[, get(cid.field)], na.rm = T)
+                           loose.ed[, (cid.field) := 1:.N + max.cid]
                            loose.ed[, class := '']
 
                            if (!is.null(annotations))

inst/extdata/anatomy.json

@@ -0,0 +1,62 @@
+[
+  {
+    "sample": "mypair",
+    "x": 0.33634716658325137,
+    "y": 0.22019120743756065
+  },
+  {
+    "sample": "mypair2",
+    "x": 0.4075275393996103,
+    "y": 0.2523906292502009
+  },
+  {
+    "sample": "J",
+    "x": 0.367271614907495,
+    "y": 0.2732773509729865
+  },
+  {
+    "sample": "K",
+    "x": 0.3412517649786515,
+    "y": 0.3080960805908625
+  },
+  {
+    "sample": "D",
+    "x": 0.5376586370853564,
+    "y": 0.3359488062611934
+  },
+  {
+    "sample": "I",
+    "x": 0.608870857943244,
+    "y": 0.33419883768441944
+  },
+  {
+    "sample": "E",
+    "x": 0.4664782642689975,
+    "y": 0.3516082024933575
+  },
+  {
+    "sample": "F",
+    "x": 0.32899026899015116,
+    "y": 0.3707562457592193
+  },
+  {
+    "sample": "G",
+    "x": 0.4198208834296392,
+    "y": 0.3803302673921502
+  },
+  {
+    "sample": "A",
+    "x": 0.5303017394922562,
+    "y": 0.4299390540137285
+  },
+  {
+    "sample": "L",
+    "x": 0.8912037460940367,
+    "y": 0.5039119192719399
+  },
+  {
+    "sample": "B",
+    "x": 0.5401109362830565,
+    "y": 0.5065312270771757
+  }
+]

tests/testthat/test_jsUtils.R

@@ -86,6 +86,9 @@ bad.kag = list(not_segstats = '')
 bad.kag.fn = paste0(tmpdir, '/bad-kag.rds')
 saveRDS(bad.kag, bad.kag.fn)
 
+myfigure = system.file('extdata', 'figure.png', package="gGnome")
+mycoord = system.file('extdata', 'anatomy.json', package="gGnome") 
+
 js_data = data.table(sample = 'mypair', coverage = cov.fn, graph = gg.rds, kag = kag.fn, bad.kag = bad.kag.fn)
 test_that('gen_js_instance', {
 
@@ -131,6 +134,10 @@ test_that('gen_js_instance', {
                 annotation = NULL,
                 ncn.gr = ncn.gr,
                 dataset_name = 'test',
+                figure = myfigure,
+                coordinates = mycoord,
+                nfields = 'eslack.out',
+                efields = 'tier'
                 )
 
     # test adding more data and also test what happens when the cov.field is NA (we expect a warning about skipping the coverage generation)
@@ -145,7 +152,7 @@ test_that('gen_js_instance', {
                     dataset_name = 'test',
                     ))
 
-    # re-run without adding a new samples, but with adding tree (so should just update the datafiles)
+    # re-run without adding new samples, but with adding tree (so should just update the datafiles)
     # also adding connections.associations
     pgv(data.table(sample = 'mypair2', coverage = cov.fn, graph = gg.rds),
                     outdir = paste0(tmpdir, '/PGV'),
@@ -194,6 +201,8 @@ test_that('gen_js_instance', {
                     dataset_name = 'test'
                     ))
 
+    # test invalid png
+    expect_error(png2pgv('no-such-file'))
 
 })