diff --git a/DESCRIPTION b/DESCRIPTION index 2fb2b38f..4744e1da 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: toxEval Type: Package Title: ToxCast Evaluations -Version: 1.0.0 -Date: 2018-07-31 +Version: 1.0.1 +Date: 2018-09-05 Authors@R: c(person("Laura", "DeCicco", role = c("aut","cre"), email = "ldecicco@usgs.gov"), diff --git a/README.Rmd b/README.Rmd index a554cd7c..b3cec6d6 100644 --- a/README.Rmd +++ b/README.Rmd @@ -76,8 +76,9 @@ plot_stacks <- plot_tox_stacks(chemicalSummary, plot_stacks ###################################### plot_heat <- plot_tox_heatmap(chemicalSummary, - tox_list$chem_site, - category = "Chemical") + tox_list$chem_site, + category = "Chemical Class", + font_size = 7) plot_heat ``` diff --git a/README.md b/README.md index 2f57ba91..cbbfb725 100644 --- a/README.md +++ b/README.md @@ -69,8 +69,9 @@ plot_stacks ``` r ###################################### plot_heat <- plot_tox_heatmap(chemicalSummary, - tox_list$chem_site, - category = "Chemical") + tox_list$chem_site, + category = "Chemical Class", + font_size = 7) plot_heat ``` diff --git a/docs/CONDUCT.html b/docs/CONDUCT.html index 0333c87d..d600aa43 100644 --- a/docs/CONDUCT.html +++ b/docs/CONDUCT.html @@ -61,7 +61,7 @@ toxEval - 1.0.0 + 1.0.1 diff --git a/docs/DISCLAIMER.html b/docs/DISCLAIMER.html index 4da93325..fc417c6b 100644 --- a/docs/DISCLAIMER.html +++ b/docs/DISCLAIMER.html @@ -61,7 +61,7 @@ toxEval - 1.0.0 + 1.0.1 diff --git a/docs/articles/Introduction.html b/docs/articles/Introduction.html index dc196dff..01631d56 100644 --- a/docs/articles/Introduction.html +++ b/docs/articles/Introduction.html @@ -30,7 +30,7 @@ toxEval - 1.0.0 + 1.0.1 @@ -81,7 +81,7 @@

Introduction to toxEval

-

06 August, 2018

+

05 September, 2018

diff --git a/docs/articles/PrepareData.html b/docs/articles/PrepareData.html index fcac090e..0cb6bd6e 100644 --- a/docs/articles/PrepareData.html +++ b/docs/articles/PrepareData.html @@ -30,7 +30,7 @@ toxEval - 1.0.0 + 1.0.1
@@ -81,7 +81,7 @@

Preparing toxEval Data

-

06 August, 2018

+

05 September, 2018

diff --git a/docs/articles/basicWorkflow.html b/docs/articles/basicWorkflow.html index a7e3bdef..5f1376cf 100644 --- a/docs/articles/basicWorkflow.html +++ b/docs/articles/basicWorkflow.html @@ -30,7 +30,7 @@ toxEval - 1.0.0 + 1.0.1
@@ -84,12 +84,12 @@ -
+

Basic Workflow

-

06 August, 2018

+

05 September, 2018

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return; + var latLng = e.target.getLatLng ? e.target.getLatLng() : e.latlng; + if (latLng) { + // retrieve only lat, lon values to remove prototype + // and extra parameters added by 3rd party modules + // these objects are for json serialization, not javascript + var latLngVal = _leaflet2.default.latLng(latLng); // make sure it has consistent shape + latLng = { lat: latLngVal.lat, lng: latLngVal.lng }; + } var eventInfo = _jquery2.default.extend({ id: layerId, ".nonce": Math.random() // force reactivity - }, group !== null ? { group: group } : null, e.target.getLatLng ? e.target.getLatLng() : e.latlng, extraInfo); + }, group !== null ? { group: group } : null, latLng, extraInfo); _shiny2.default.onInputChange(mapId + "_" + eventName, eventInfo); }; diff --git a/docs/articles/basicWorkflow_files/leaflet-binding-2.0.1/leaflet.yaml b/docs/articles/basicWorkflow_files/leaflet-binding-2.0.2/leaflet.yaml similarity index 100% rename from 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docs/articles/basicWorkflow_files/leaflet-binding-2.0.1/plugins/leaflet-providers-plugin/leaflet-providers-plugin.js rename to docs/articles/basicWorkflow_files/leaflet-binding-2.0.2/plugins/leaflet-providers-plugin/leaflet-providers-plugin.js diff --git a/docs/articles/basicWorkflow_files/leaflet-providers-plugin-2.0.1/leaflet-providers-plugin.js b/docs/articles/basicWorkflow_files/leaflet-providers-plugin-2.0.2/leaflet-providers-plugin.js similarity index 100% rename from docs/articles/basicWorkflow_files/leaflet-providers-plugin-2.0.1/leaflet-providers-plugin.js rename to docs/articles/basicWorkflow_files/leaflet-providers-plugin-2.0.2/leaflet-providers-plugin.js diff --git a/docs/articles/index.html b/docs/articles/index.html index dfa1a267..64dd91ad 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -61,7 +61,7 @@ toxEval - 1.0.0 + 1.0.1
diff --git a/docs/articles/shinyApp.html b/docs/articles/shinyApp.html index 869603a0..a57a9ca0 100644 --- a/docs/articles/shinyApp.html +++ b/docs/articles/shinyApp.html @@ -30,7 +30,7 @@ toxEval - 1.0.0 + 1.0.1
@@ -81,7 +81,7 @@

Shiny App

-

06 August, 2018

+

05 September, 2018

diff --git a/docs/authors.html b/docs/authors.html index abe57054..79f53001 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -61,7 +61,7 @@ toxEval - 1.0.0 + 1.0.1
diff --git a/docs/favicon.ico b/docs/favicon.ico index a61770b2..a4f2ea24 100644 Binary files a/docs/favicon.ico and b/docs/favicon.ico differ diff --git a/docs/index.html b/docs/index.html index 59417c13..90abb7a3 100644 --- a/docs/index.html +++ b/docs/index.html @@ -30,7 +30,7 @@ toxEval - 1.0.0 + 1.0.1
@@ -131,8 +131,9 @@ 

######################################
 plot_heat <- plot_tox_heatmap(chemicalSummary, 
-                               tox_list$chem_site, 
-                               category = "Chemical")
+                              tox_list$chem_site, 
+                              category = "Chemical Class",
+                              font_size = 7)
 plot_heat

This code opens up the example file, loads it into a toxEval object, grabs the pertinent ToxCast information, and creates a “chemicalSummary” data frame that is used in many of the plot and table functions.

diff --git a/docs/logo.png b/docs/logo.png index fcc63301..5b1eb090 100644 Binary files a/docs/logo.png and b/docs/logo.png differ diff --git a/docs/reference/ToxCast_ACC.html b/docs/reference/ToxCast_ACC.html index af60c7e3..6c886f95 100644 --- a/docs/reference/ToxCast_ACC.html +++ b/docs/reference/ToxCast_ACC.html @@ -69,7 +69,7 @@ toxEval - 1.0.0 + 1.0.1

diff --git a/docs/reference/clean_endPoint_info.html b/docs/reference/clean_endPoint_info.html index 5b4cf04b..be4f00a0 100644 --- a/docs/reference/clean_endPoint_info.html +++ b/docs/reference/clean_endPoint_info.html @@ -70,7 +70,7 @@ toxEval - 1.0.0 + 1.0.1 diff --git a/docs/reference/createLink.html b/docs/reference/createLink.html index a01c5ace..87a6605a 100644 --- a/docs/reference/createLink.html +++ b/docs/reference/createLink.html @@ -63,7 +63,7 @@ toxEval - 1.0.0 + 1.0.1 diff --git a/docs/reference/create_toxEval.html b/docs/reference/create_toxEval.html index 7a4818fc..c5e5d723 100644 --- a/docs/reference/create_toxEval.html +++ b/docs/reference/create_toxEval.html @@ -68,7 +68,7 @@ toxEval - 1.0.0 + 1.0.1 diff --git a/docs/reference/end_point_info.html b/docs/reference/end_point_info.html index 6f3aa65d..391f5a07 100644 --- a/docs/reference/end_point_info.html +++ b/docs/reference/end_point_info.html @@ -69,7 +69,7 @@ toxEval - 1.0.0 + 1.0.1 diff --git a/docs/reference/endpoint_hits_DT.html b/docs/reference/endpoint_hits_DT.html index a8f2e61a..aa66924f 100644 --- a/docs/reference/endpoint_hits_DT.html +++ b/docs/reference/endpoint_hits_DT.html @@ -70,7 +70,7 @@ toxEval - 1.0.0 + 1.0.1 diff --git a/docs/reference/explore_endpoints.html b/docs/reference/explore_endpoints.html index 11f5a25b..8aab7d91 100644 --- a/docs/reference/explore_endpoints.html +++ b/docs/reference/explore_endpoints.html @@ -68,7 +68,7 @@ toxEval - 1.0.0 + 1.0.1 diff --git a/docs/reference/figures/logo.png b/docs/reference/figures/logo.png index fcc63301..5b1eb090 100644 Binary files a/docs/reference/figures/logo.png and b/docs/reference/figures/logo.png differ diff --git a/docs/reference/figures/toxEval.png b/docs/reference/figures/toxEval.png new file mode 100644 index 00000000..8d545285 Binary files /dev/null and b/docs/reference/figures/toxEval.png differ diff --git a/docs/reference/figures/unnamed-chunk-4-1.png b/docs/reference/figures/unnamed-chunk-4-1.png index 506af63c..39b83568 100644 Binary files a/docs/reference/figures/unnamed-chunk-4-1.png and b/docs/reference/figures/unnamed-chunk-4-1.png differ diff --git a/docs/reference/figures/unnamed-chunk-4-2.png b/docs/reference/figures/unnamed-chunk-4-2.png index 6c10ca37..43d5ca7e 100644 Binary files a/docs/reference/figures/unnamed-chunk-4-2.png and b/docs/reference/figures/unnamed-chunk-4-2.png differ diff --git a/docs/reference/figures/unnamed-chunk-4-3.png b/docs/reference/figures/unnamed-chunk-4-3.png index 44ed3274..308679b9 100644 Binary files a/docs/reference/figures/unnamed-chunk-4-3.png and b/docs/reference/figures/unnamed-chunk-4-3.png differ diff --git a/docs/reference/filter_groups.html b/docs/reference/filter_groups.html index e21ad426..5dcddcbe 100644 --- a/docs/reference/filter_groups.html +++ b/docs/reference/filter_groups.html @@ -70,7 +70,7 @@ toxEval - 1.0.0 + 1.0.1 diff --git a/docs/reference/get_ACC.html b/docs/reference/get_ACC.html index f720a9d9..cad66b3e 100644 --- a/docs/reference/get_ACC.html +++ b/docs/reference/get_ACC.html @@ -64,7 +64,7 @@ toxEval - 1.0.0 + 1.0.1 diff --git a/docs/reference/get_chemical_summary.html b/docs/reference/get_chemical_summary.html index 5cea526c..6ff29049 100644 --- a/docs/reference/get_chemical_summary.html +++ b/docs/reference/get_chemical_summary.html @@ -67,7 +67,7 @@ toxEval - 1.0.0 + 1.0.1 diff --git a/docs/reference/hits_by_groupings_DT.html b/docs/reference/hits_by_groupings_DT.html index 8cf290d4..c627cc75 100644 --- a/docs/reference/hits_by_groupings_DT.html +++ b/docs/reference/hits_by_groupings_DT.html @@ -70,7 +70,7 @@ toxEval - 1.0.0 + 1.0.1 diff --git a/docs/reference/hits_summary_DT.html b/docs/reference/hits_summary_DT.html index 3a6b8e58..1cd06f34 100644 --- a/docs/reference/hits_summary_DT.html +++ b/docs/reference/hits_summary_DT.html @@ -70,7 +70,7 @@ toxEval - 1.0.0 + 1.0.1 diff --git a/docs/reference/index.html b/docs/reference/index.html index bcc1e682..a3d2d9ae 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -61,7 +61,7 @@ toxEval - 1.0.0 + 1.0.1 diff --git a/docs/reference/make_tox_map.html b/docs/reference/make_tox_map.html index 0182c87e..47aefc31 100644 --- a/docs/reference/make_tox_map.html +++ b/docs/reference/make_tox_map.html @@ -68,7 +68,7 @@ toxEval - 1.0.0 + 1.0.1 diff --git a/docs/reference/plot_tox_boxplots-1.png b/docs/reference/plot_tox_boxplots-1.png index 6c3126c9..121a37b2 100644 Binary files a/docs/reference/plot_tox_boxplots-1.png and b/docs/reference/plot_tox_boxplots-1.png differ diff --git a/docs/reference/plot_tox_boxplots-2.png b/docs/reference/plot_tox_boxplots-2.png index b8d177bb..43a3922f 100644 Binary files a/docs/reference/plot_tox_boxplots-2.png and b/docs/reference/plot_tox_boxplots-2.png differ diff --git a/docs/reference/plot_tox_boxplots-3.png b/docs/reference/plot_tox_boxplots-3.png index 5d6fda9b..06fe555b 100644 Binary files a/docs/reference/plot_tox_boxplots-3.png and b/docs/reference/plot_tox_boxplots-3.png differ diff --git a/docs/reference/plot_tox_boxplots-4.png b/docs/reference/plot_tox_boxplots-4.png index 1a72f704..74d75f1c 100644 Binary files a/docs/reference/plot_tox_boxplots-4.png and b/docs/reference/plot_tox_boxplots-4.png differ diff --git a/docs/reference/plot_tox_boxplots.html b/docs/reference/plot_tox_boxplots.html index 6c027f21..8f4700e2 100644 --- a/docs/reference/plot_tox_boxplots.html +++ b/docs/reference/plot_tox_boxplots.html @@ -71,7 +71,7 @@ toxEval - 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1.0.0 + 1.0.1 diff --git a/docs/reference/remove_flags.html b/docs/reference/remove_flags.html index 9c0a8ca5..18619e24 100644 --- a/docs/reference/remove_flags.html +++ b/docs/reference/remove_flags.html @@ -81,7 +81,7 @@ toxEval - 1.0.0 + 1.0.1 diff --git a/docs/reference/summary.toxEval.html b/docs/reference/summary.toxEval.html index fa7b384d..7d7ceba4 100644 --- a/docs/reference/summary.toxEval.html +++ b/docs/reference/summary.toxEval.html @@ -67,7 +67,7 @@ toxEval - 1.0.0 + 1.0.1 diff --git a/docs/reference/toxEval-package.html b/docs/reference/toxEval-package.html index cbf29e52..d010e7e9 100644 --- a/docs/reference/toxEval-package.html +++ b/docs/reference/toxEval-package.html @@ -72,7 +72,7 @@ toxEval - 1.0.0 + 1.0.1 diff --git a/docs/reference/tox_chemicals.html b/docs/reference/tox_chemicals.html index acc0abf4..76c92edb 100644 --- a/docs/reference/tox_chemicals.html +++ b/docs/reference/tox_chemicals.html @@ -70,7 +70,7 @@ toxEval - 1.0.0 + 1.0.1 diff --git a/hexSticker.R b/hexSticker.R index 5f3ea9bd..0c9b5649 100644 --- a/hexSticker.R +++ b/hexSticker.R @@ -1,13 +1,14 @@ library(hexSticker) -outline = "#EAEBEF" -background = "#000080" -sticker("./man/figures/tears.png", - package = "toxEval", +outline = "#000080" +background = "white" +sticker("./man/figures/toxEval.png", + package = "", h_fill = background, h_color = outline, - p_size = 25, - s_width = 0.35, - s_height = 0.35, + s_y = 1.1, + p_size = 1000, + s_width = 0.8, + s_height = 0.8, s_x = 1, filename = "./man/figures/logo.png") diff --git a/man/figures/logo.png b/man/figures/logo.png index fcc63301..5b1eb090 100644 Binary files a/man/figures/logo.png and b/man/figures/logo.png differ diff --git a/man/figures/tears.png b/man/figures/tears.png deleted file mode 100644 index 3825d1e4..00000000 Binary files a/man/figures/tears.png and /dev/null differ diff --git a/man/figures/toxEval.png b/man/figures/toxEval.png new file mode 100644 index 00000000..8d545285 Binary files /dev/null and b/man/figures/toxEval.png differ diff --git a/man/figures/unnamed-chunk-4-1.png b/man/figures/unnamed-chunk-4-1.png index 506af63c..39b83568 100644 Binary files a/man/figures/unnamed-chunk-4-1.png and b/man/figures/unnamed-chunk-4-1.png differ diff --git a/man/figures/unnamed-chunk-4-2.png b/man/figures/unnamed-chunk-4-2.png index 6c10ca37..43d5ca7e 100644 Binary files a/man/figures/unnamed-chunk-4-2.png and b/man/figures/unnamed-chunk-4-2.png differ diff --git a/man/figures/unnamed-chunk-4-3.png b/man/figures/unnamed-chunk-4-3.png index 44ed3274..308679b9 100644 Binary files a/man/figures/unnamed-chunk-4-3.png and b/man/figures/unnamed-chunk-4-3.png differ