digit changes_ download plot added ind number

phuse-org · Feb 22, 2023 · e39dcd4 · e39dcd4
1 parent 038cbf7
commit e39dcd4
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Showing 4 changed files with 15 additions and 18 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -14,7 +14,7 @@ url: https://github.com/phuse-org/toxSummary
 BugReports: https://github.com/phuse-org/toxSummary/issues
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.2.1
 Imports: 
     cicerone,
     data.table,
@@ -41,4 +41,3 @@ Depends:
 Suggests: 
     knitr,
     rmarkdown
-VignetteBuilder: knitr
diff --git a/R/tox_summary_new_UI.R b/R/tox_summary_new_UI.R
@@ -1131,10 +1131,10 @@ values$Findings <- ''
             SM_MRHD <- HED/(Data[["Clinical Information"]][["MRHD"]][["MRHDAUC"]])
           } else {SM_MRHD <- NA}
         }
-        plotData[i, "HED_value"]<- round(HED, digits = 2) ##for table 03
-        plotData[i, "SM"] <- round(HED/humanDose, 2)
-        plotData[i, "SM_start_dose"] <- round(SM_start, digits = 2)
-        plotData[i, "SM_MRHD"] <- round(SM_MRHD, digits = 2)
+        plotData[i, "HED_value"]<- round(HED, digits = 3) ##for table 03
+        plotData[i, "SM"] <- round(HED/humanDose, 3)
+        plotData[i, "SM_start_dose"] <- round(SM_start, digits = 3)
+        plotData[i, "SM_MRHD"] <- round(SM_MRHD, digits = 3)
       }
     }
     return(plotData)
@@ -1745,7 +1745,11 @@ values$Findings <- ''
         ggplot2::guides(fill = ggplot2::guide_legend(override.aes = ggplot2::aes(label = "")))
 
       ggiraph::girafe(code = print(p+q+ patchwork::plot_layout(ncol = 2, widths = c(3,1))),
-             options = list(ggiraph::opts_tooltip(css = tooltip_css)),
+             options = list(ggiraph::opts_tooltip(css = tooltip_css),
+                            ggiraph::opts_toolbar(
+                              pngname = paste0(basename(unlist(strsplit(input$selectData, ".rds"))),
+                                               "_downloaded on ",
+                                               date()))),
              fonts = list(sans= "Roboto"),
              width_svg = 18, height_svg = plotHeight())
     }

diff --git a/vignettes/Introduction.Rmd b/vignettes/Introduction.Rmd
@@ -70,7 +70,6 @@ When user choose to connect to database, user need one more csv file that map
 studies to a corresponding number. An example file can be found here 
 [link](https://github.com/phuse-org/toxSummary/blob/master/test_data/IND_with_studies_2.csv).
 
-
 |                      |             |             |
 |:--------------------:|:-----------:|:-----------:|
 | **application_type** | **IND_num** | **studyID** |

diff --git a/vignettes/articles/Exposure-Margin.Rmd b/vignettes/articles/Exposure-Margin.Rmd
@@ -15,13 +15,11 @@ library(toxSummary)
 
 ## Exposure Margin Calculation:
 This is an example of how exposure margin calculated for dog 4 week (IV) study using 
-body surface area (BSA) formula.    
-- Clinical information: Human Proposed "Start Dose": 1.5 mg/day   
-- Dog to Human conversion factor = 1.8   
-- HED = Human Equivalent Dose   
-- Dog 4 week (IV) study:    
-
-
+body surface area (BSA) formula.
+Clinical information: Human Proposed "Start Dose": 1.5 mg/day
+Dog to Human conversion factor = 1.8
+HED = Human Equivalent Dose
+Dog 4 week (IV) study:
 +---------------------------------------+-------------------+-----------------+-----------------+
 | Animal Dose ---\>                     | 0.25 mg/kg/day    | 0.8 mg/kg/day   | 2.5 mg/kg/day   |
 +---------------------------------------+-------------------+-----------------+-----------------+
@@ -44,10 +42,7 @@ body surface area (BSA) formula.
 | Exposure Margin                       | 5.6               | 18              | 56              |
 +---------------------------------------+-------------------+-----------------+-----------------+
 
-
 : Exposure Margin Calculation
-
-
 ![Clinical](https://user-images.githubusercontent.com/31291716/215581375-b351f896-2aa8-4097-9b41-96dc290be739.jpg)