README.md
In meerapatelmd/chariotViz: Visualize the OMOP Vocabularies
chariotViz
Visualize the OMOP vocabularies from multiple dimensions using the
DiagrammeR package.
Installation
You can install the development version from
GitHub with:
# install.packages("devtools")
devtools::install_github("meerapatelmd/chariotViz")
Prerequisites
- OMOP vocabularies loaded into a Postgres instance (see
setupAthena).
- R.cache R package that caches the query resultsets.
How It Works
S4 Classes
The raw OMOP data is fetched from the Postgres instance.
library(chariotViz)
omop_rels <-
fetch_omop_relationships(version_key = get_version_key())
The fetched data belongs to the omop.relationships S4 class.
class(omop_rels)
#> [1] "omop.relationships"
#> attr(,"package")
#> [1] "chariotViz"
The omop.relationship class is converted to the nodes.and.edges S4
class.
omop_ne <-
create_nodes_and_edges(omop_relationships = omop_rels)
class(omop_ne)
#> [1] "nodes.and.edges"
#> attr(,"package")
#> [1] "chariotViz"
From nodes.and.edges, an omop.graph S4 class object can be
constructed.
omop_gr <-
construct_graph(omop_ne)
#> Warning: Unknown or uninitialised column: `id`.
class(omop_gr)
#> [1] "omop.graph"
#> attr(,"package")
#> [1] "chariotViz"
The omop.graph can then be rendered, but due to its size, force must
be set to TRUE in order to do so.
chariotViz(omop_gr)
#> ─────────────────────
#> n nodes n edges
#> ─────────────────────
#> 650 9030
#> ─────────────────────
#> There are 650 nodes and 9030 edges.
#> To render anyways, set `force` to TRUE.
Subsetting
An omop.relationships object can be subset using tidyverse-style
filtering. Here, I am subsetting for all the relationships associated
with Cancer Modifier. Since the node count is below the threshold set by
default in the chariotViz function, the graph renders automatically
and without having to set force to TRUE.
cancer_modifier_relationships <-
omop_rels %>%
filter_omop_relationships(
vocabulary_id_1 == "Cancer Modifier")
cancer_modifier_ne <-
cancer_modifier_relationships %>%
create_nodes_and_edges()
cancer_modifier_graph <-
cancer_modifier_ne %>%
construct_graph()
#> Warning: Unknown or uninitialised column: `id`.
chariotViz(cancer_modifier_graph)
#> ─────────────────────
#> n nodes n edges
#> ─────────────────────
#> 15 14
#> ─────────────────────
Adding Pizzaz
The visualization is nice, but it needs a little oomph. A tooltip and
visualization attributes can be added to the nodes.and.edges class
object prior to graph construction. (Note that the tooltip is not
rendering in this README, but view articles to see examples.)
cancer_modifier_relationships <-
omop_rels %>%
filter_omop_relationships(
vocabulary_id_1 == "Cancer Modifier")
cancer_modifier_ne <-
cancer_modifier_relationships %>%
create_nodes_and_edges() %>%
add_tooltip()
cancer_modifier_graph <-
cancer_modifier_ne %>%
construct_graph()
#> Warning: Unknown or uninitialised column: `id`.
chariotViz(cancer_modifier_graph)
#> ─────────────────────
#> n nodes n edges
#> ─────────────────────
#> 15 14
#> ─────────────────────
In addition to the tooltip, the way the nodes and edges appear can also
be customized.
cancer_modifier_relationships <-
omop_rels %>%
filter_omop_relationships(
vocabulary_id_1 == "Cancer Modifier")
cancer_modifier_ne <-
cancer_modifier_relationships %>%
create_nodes_and_edges() %>%
add_tooltip() %>%
map_node_attributes() %>%
map_edge_attributes()
#> ══
#> Node Attributes ════════════════════════════════════════
#> ℹ Shape from: standard_concept
#> ✓ All 2 unique values mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> S circle
#> NA circle
#> ───────────────────────
#> ℹ Style from: standard_concept
#> ✓ All 2 unique values mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> S filled
#> NA filled
#> ───────────────────────
#> ℹ Color from: standard_concept
#> ✓ All 2 unique values mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> S black
#> NA white
#> ───────────────────────
#> ℹ Fillcolor from: vocabulary_id
#> ! 3 values not mapped: CIM10, KCD7, and Read. Mapping to `other` value 'gray20'.
#> ℹ Fontcolor from: standard_concept
#> ✓ All 2 unique values mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> S black
#> NA gray40
#> ───────────────────────
#> ℹ 3 constant attributes added: fontsize, width, and height.
#> ✓ All 1 unique value mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> 0 solid
#> ───────────────────────
#> ✓ All 1 unique value mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> OMOP black
#> ───────────────────────
#> ✓ All 1 unique value mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> 0 2
#> ───────────────────────
#> ✓ All 1 unique value mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> 0 vee
#> ───────────────────────
#> ℹ 2 constant attributes added: fontsize and len.
cancer_modifier_graph <-
cancer_modifier_ne %>%
construct_graph()
#> Warning: Unknown or uninitialised column: `id`.
chariotViz(cancer_modifier_graph)
#> ─────────────────────
#> n nodes n edges
#> ─────────────────────
#> 15 14
#> ─────────────────────
Resizing
Due to the large number of other relationships for Cancer Modifier, the
height needs to be increased to make it more legible.
chariotViz(cancer_modifier_graph,
height = 1500,
width = 500)
#> ─────────────────────
#> n nodes n edges
#> ─────────────────────
#> 15 14
#> ─────────────────────
Reconfiguring
The direction can also be reconfigured.
cancer_modifier_relationships <-
omop_rels %>%
filter_omop_relationships(
vocabulary_id_1 == "Cancer Modifier")
cancer_modifier_ne <-
cancer_modifier_relationships %>%
create_nodes_and_edges() %>%
add_tooltip() %>%
map_node_attributes() %>%
map_edge_attributes()
#> ══
#> Node Attributes ════════════════════════════════════════
#> ℹ Shape from: standard_concept
#> ✓ All 2 unique values mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> S circle
#> NA circle
#> ───────────────────────
#> ℹ Style from: standard_concept
#> ✓ All 2 unique values mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> S filled
#> NA filled
#> ───────────────────────
#> ℹ Color from: standard_concept
#> ✓ All 2 unique values mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> S black
#> NA white
#> ───────────────────────
#> ℹ Fillcolor from: vocabulary_id
#> ! 3 values not mapped: CIM10, KCD7, and Read. Mapping to `other` value 'gray20'.
#> ℹ Fontcolor from: standard_concept
#> ✓ All 2 unique values mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> S black
#> NA gray40
#> ───────────────────────
#> ℹ 3 constant attributes added: fontsize, width, and height.
#> ✓ All 1 unique value mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> 0 solid
#> ───────────────────────
#> ✓ All 1 unique value mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> OMOP black
#> ───────────────────────
#> ✓ All 1 unique value mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> 0 2
#> ───────────────────────
#> ✓ All 1 unique value mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> 0 vee
#> ───────────────────────
#> ℹ 2 constant attributes added: fontsize and len.
cancer_modifier_graph <-
cancer_modifier_ne %>%
construct_graph(attr_theme = "tb")
#> Warning: Unknown or uninitialised column: `id`.
chariotViz(cancer_modifier_graph,
width = 2500,
height = 500)
#> ─────────────────────
#> n nodes n edges
#> ─────────────────────
#> 15 14
#> ─────────────────────
Adding Example Concepts
set.seed(seed = 1)
cancer_modifier_relationships <-
omop_rels %>%
filter_omop_relationships(
vocabulary_id_1 == "Cancer Modifier")
cancer_modifier_ne <-
cancer_modifier_relationships %>%
create_nodes_and_edges() %>%
add_tooltip() %>%
map_node_attributes() %>%
map_edge_attributes()
#> ══
#> Node Attributes ════════════════════════════════════════
#> ℹ Shape from: standard_concept
#> ✓ All 2 unique values mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> S circle
#> NA circle
#> ───────────────────────
#> ℹ Style from: standard_concept
#> ✓ All 2 unique values mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> S filled
#> NA filled
#> ───────────────────────
#> ℹ Color from: standard_concept
#> ✓ All 2 unique values mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> S black
#> NA white
#> ───────────────────────
#> ℹ Fillcolor from: vocabulary_id
#> ! 3 values not mapped: CIM10, KCD7, and Read. Mapping to `other` value 'gray20'.
#> ℹ Fontcolor from: standard_concept
#> ✓ All 2 unique values mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> S black
#> NA gray40
#> ───────────────────────
#> ℹ 3 constant attributes added: fontsize, width, and height.
#> ✓ All 1 unique value mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> 0 solid
#> ───────────────────────
#> ✓ All 1 unique value mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> OMOP black
#> ───────────────────────
#> ✓ All 1 unique value mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> 0 2
#> ───────────────────────
#> ✓ All 1 unique value mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> 0 vee
#> ───────────────────────
#> ℹ 2 constant attributes added: fontsize and len.
cancer_modifier_graph <-
cancer_modifier_ne %>%
construct_graph() %>%
append_concept_examples(sample_size = 3)
#> Warning: Unknown or uninitialised column: `id`.
#> Warning: Unknown or uninitialised column: `id`.
#> Warning: Unknown or uninitialised column: `id`.
chariotViz(cancer_modifier_graph)
#> ─────────────────────
#> n nodes n edges
#> ─────────────────────
#> 60 59
#> ─────────────────────
#> There are 60 nodes and 59 edges.
#> To render anyways, set `force` to TRUE.
chariotViz(cancer_modifier_graph,
force = TRUE,
height = 2500,
width = 700)
#> ─────────────────────
#> n nodes n edges
#> ─────────────────────
#> 60 59
#> ─────────────────────
meerapatelmd/chariotViz documentation built on Dec. 21, 2021, 4:53 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
chariotViz
Visualize the OMOP vocabularies from multiple dimensions using the DiagrammeR package.
Installation
You can install the development version from GitHub with:
# install.packages("devtools")
devtools::install_github("meerapatelmd/chariotViz")
Prerequisites
- OMOP vocabularies loaded into a Postgres instance (see setupAthena).
- R.cache R package that caches the query resultsets.
How It Works
S4 Classes
The raw OMOP data is fetched from the Postgres instance.
library(chariotViz)
omop_rels <-
fetch_omop_relationships(version_key = get_version_key())
The fetched data belongs to the omop.relationships S4 class.
class(omop_rels)
#> [1] "omop.relationships"
#> attr(,"package")
#> [1] "chariotViz"
The omop.relationship class is converted to the nodes.and.edges S4
class.
omop_ne <-
create_nodes_and_edges(omop_relationships = omop_rels)
class(omop_ne)
#> [1] "nodes.and.edges"
#> attr(,"package")
#> [1] "chariotViz"
From nodes.and.edges, an omop.graph S4 class object can be
constructed.
omop_gr <-
construct_graph(omop_ne)
#> Warning: Unknown or uninitialised column: `id`.
class(omop_gr)
#> [1] "omop.graph"
#> attr(,"package")
#> [1] "chariotViz"
The omop.graph can then be rendered, but due to its size, force must
be set to TRUE in order to do so.
chariotViz(omop_gr)
#> ─────────────────────
#> n nodes n edges
#> ─────────────────────
#> 650 9030
#> ─────────────────────
#> There are 650 nodes and 9030 edges.
#> To render anyways, set `force` to TRUE.
Subsetting
An omop.relationships object can be subset using tidyverse-style
filtering. Here, I am subsetting for all the relationships associated
with Cancer Modifier. Since the node count is below the threshold set by
default in the chariotViz function, the graph renders automatically
and without having to set force to TRUE.
cancer_modifier_relationships <-
omop_rels %>%
filter_omop_relationships(
vocabulary_id_1 == "Cancer Modifier")
cancer_modifier_ne <-
cancer_modifier_relationships %>%
create_nodes_and_edges()
cancer_modifier_graph <-
cancer_modifier_ne %>%
construct_graph()
#> Warning: Unknown or uninitialised column: `id`.
chariotViz(cancer_modifier_graph)
#> ─────────────────────
#> n nodes n edges
#> ─────────────────────
#> 15 14
#> ─────────────────────
Adding Pizzaz
The visualization is nice, but it needs a little oomph. A tooltip and
visualization attributes can be added to the nodes.and.edges class
object prior to graph construction. (Note that the tooltip is not
rendering in this README, but view articles to see examples.)
cancer_modifier_relationships <-
omop_rels %>%
filter_omop_relationships(
vocabulary_id_1 == "Cancer Modifier")
cancer_modifier_ne <-
cancer_modifier_relationships %>%
create_nodes_and_edges() %>%
add_tooltip()
cancer_modifier_graph <-
cancer_modifier_ne %>%
construct_graph()
#> Warning: Unknown or uninitialised column: `id`.
chariotViz(cancer_modifier_graph)
#> ─────────────────────
#> n nodes n edges
#> ─────────────────────
#> 15 14
#> ─────────────────────
In addition to the tooltip, the way the nodes and edges appear can also be customized.
cancer_modifier_relationships <-
omop_rels %>%
filter_omop_relationships(
vocabulary_id_1 == "Cancer Modifier")
cancer_modifier_ne <-
cancer_modifier_relationships %>%
create_nodes_and_edges() %>%
add_tooltip() %>%
map_node_attributes() %>%
map_edge_attributes()
#> ══
#> Node Attributes ════════════════════════════════════════
#> ℹ Shape from: standard_concept
#> ✓ All 2 unique values mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> S circle
#> NA circle
#> ───────────────────────
#> ℹ Style from: standard_concept
#> ✓ All 2 unique values mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> S filled
#> NA filled
#> ───────────────────────
#> ℹ Color from: standard_concept
#> ✓ All 2 unique values mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> S black
#> NA white
#> ───────────────────────
#> ℹ Fillcolor from: vocabulary_id
#> ! 3 values not mapped: CIM10, KCD7, and Read. Mapping to `other` value 'gray20'.
#> ℹ Fontcolor from: standard_concept
#> ✓ All 2 unique values mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> S black
#> NA gray40
#> ───────────────────────
#> ℹ 3 constant attributes added: fontsize, width, and height.
#> ✓ All 1 unique value mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> 0 solid
#> ───────────────────────
#> ✓ All 1 unique value mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> OMOP black
#> ───────────────────────
#> ✓ All 1 unique value mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> 0 2
#> ───────────────────────
#> ✓ All 1 unique value mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> 0 vee
#> ───────────────────────
#> ℹ 2 constant attributes added: fontsize and len.
cancer_modifier_graph <-
cancer_modifier_ne %>%
construct_graph()
#> Warning: Unknown or uninitialised column: `id`.
chariotViz(cancer_modifier_graph)
#> ─────────────────────
#> n nodes n edges
#> ─────────────────────
#> 15 14
#> ─────────────────────
Resizing
Due to the large number of other relationships for Cancer Modifier, the height needs to be increased to make it more legible.
chariotViz(cancer_modifier_graph,
height = 1500,
width = 500)
#> ─────────────────────
#> n nodes n edges
#> ─────────────────────
#> 15 14
#> ─────────────────────
Reconfiguring
The direction can also be reconfigured.
cancer_modifier_relationships <-
omop_rels %>%
filter_omop_relationships(
vocabulary_id_1 == "Cancer Modifier")
cancer_modifier_ne <-
cancer_modifier_relationships %>%
create_nodes_and_edges() %>%
add_tooltip() %>%
map_node_attributes() %>%
map_edge_attributes()
#> ══
#> Node Attributes ════════════════════════════════════════
#> ℹ Shape from: standard_concept
#> ✓ All 2 unique values mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> S circle
#> NA circle
#> ───────────────────────
#> ℹ Style from: standard_concept
#> ✓ All 2 unique values mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> S filled
#> NA filled
#> ───────────────────────
#> ℹ Color from: standard_concept
#> ✓ All 2 unique values mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> S black
#> NA white
#> ───────────────────────
#> ℹ Fillcolor from: vocabulary_id
#> ! 3 values not mapped: CIM10, KCD7, and Read. Mapping to `other` value 'gray20'.
#> ℹ Fontcolor from: standard_concept
#> ✓ All 2 unique values mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> S black
#> NA gray40
#> ───────────────────────
#> ℹ 3 constant attributes added: fontsize, width, and height.
#> ✓ All 1 unique value mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> 0 solid
#> ───────────────────────
#> ✓ All 1 unique value mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> OMOP black
#> ───────────────────────
#> ✓ All 1 unique value mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> 0 2
#> ───────────────────────
#> ✓ All 1 unique value mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> 0 vee
#> ───────────────────────
#> ℹ 2 constant attributes added: fontsize and len.
cancer_modifier_graph <-
cancer_modifier_ne %>%
construct_graph(attr_theme = "tb")
#> Warning: Unknown or uninitialised column: `id`.
chariotViz(cancer_modifier_graph,
width = 2500,
height = 500)
#> ─────────────────────
#> n nodes n edges
#> ─────────────────────
#> 15 14
#> ─────────────────────
Adding Example Concepts
set.seed(seed = 1)
cancer_modifier_relationships <-
omop_rels %>%
filter_omop_relationships(
vocabulary_id_1 == "Cancer Modifier")
cancer_modifier_ne <-
cancer_modifier_relationships %>%
create_nodes_and_edges() %>%
add_tooltip() %>%
map_node_attributes() %>%
map_edge_attributes()
#> ══
#> Node Attributes ════════════════════════════════════════
#> ℹ Shape from: standard_concept
#> ✓ All 2 unique values mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> S circle
#> NA circle
#> ───────────────────────
#> ℹ Style from: standard_concept
#> ✓ All 2 unique values mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> S filled
#> NA filled
#> ───────────────────────
#> ℹ Color from: standard_concept
#> ✓ All 2 unique values mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> S black
#> NA white
#> ───────────────────────
#> ℹ Fillcolor from: vocabulary_id
#> ! 3 values not mapped: CIM10, KCD7, and Read. Mapping to `other` value 'gray20'.
#> ℹ Fontcolor from: standard_concept
#> ✓ All 2 unique values mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> S black
#> NA gray40
#> ───────────────────────
#> ℹ 3 constant attributes added: fontsize, width, and height.
#> ✓ All 1 unique value mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> 0 solid
#> ───────────────────────
#> ✓ All 1 unique value mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> OMOP black
#> ───────────────────────
#> ✓ All 1 unique value mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> 0 2
#> ───────────────────────
#> ✓ All 1 unique value mapped:
#> ───────────────────────
#> Attribute Value
#> ───────────────────────
#> 0 vee
#> ───────────────────────
#> ℹ 2 constant attributes added: fontsize and len.
cancer_modifier_graph <-
cancer_modifier_ne %>%
construct_graph() %>%
append_concept_examples(sample_size = 3)
#> Warning: Unknown or uninitialised column: `id`.
#> Warning: Unknown or uninitialised column: `id`.
#> Warning: Unknown or uninitialised column: `id`.
chariotViz(cancer_modifier_graph)
#> ─────────────────────
#> n nodes n edges
#> ─────────────────────
#> 60 59
#> ─────────────────────
#> There are 60 nodes and 59 edges.
#> To render anyways, set `force` to TRUE.
chariotViz(cancer_modifier_graph,
force = TRUE,
height = 2500,
width = 700)
#> ─────────────────────
#> n nodes n edges
#> ─────────────────────
#> 60 59
#> ─────────────────────
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