added HTMLTables to project. new examples, removed css color

Project.toml

@@ -24,8 +24,9 @@ julia = "1"
 
 [extras]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
+HTMLTables = "b1afcece-b80e-4563-b90e-36b4cc56d3fa"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 XLSX = "fdbf4ff8-1666-58a4-91e7-1b58723a45e0"
 
 [targets]
-test = ["Test", "CSV", "XLSX"]
+test = ["Test", "CSV", "HTMLTables", "XLSX"]

README.md

@@ -21,7 +21,119 @@ PRISMA.jl is a Julia package and [web application]() for generating checklists a
 using Pkg; Pkg.add("PRISMA")
 ```
 
-## :computer: Examples
+## Examples
+
+The `flow_diagram_df` function is needed to create flow diagram. It has three columns: `"box_num"`, `"box_lab"`, `"results"`. The `"box_num"` column determines what box the data belongs to. A `"box_label"` would be the title of the box or an exclusion reason, and the `"results"` is the number of records that was excluded, so it must have an adjacent `"box_label"`. This `DataFrame` that is returned from `flow_diagram_df` can be saved as a data file then be read back into a Julia program using the `DataFrames` package or it can be directly modified in a Julia program using functions from `DataFrames` like `push!`:
+
+```julia
+using PRISMA: flow_diagram
+using DataFrames: DataFrame, push!
+using CSV, HTMLTables, XLSX
+
+df::DataFrame = flow_diagram_df()
+
+# adding new Databases
+push!(df, (8, "Database or Register 4", 150))
+push!(df, (8, "Database or Register 5", 121))
+
+# adding new reasons for exclusion
+push!(df, (15, "Reason 4", 20))
+push!(df, (15, "Reason 5", 10))
+push!(df, (15, "Reason 6", 03))
+
+println(df)
+
+# export the data as a CSV to edit then read it back to a DataFrame
+csv_path::String = "flow_diagram.csv"
+CSV.write(csv_path, df)
+csv_df::DataFrame = CSV.read(csv_path, DataFrame)
+
+println(csv_df)
+
+# export the data as a HTML table to edit then read it back to a DataFrame
+html_path::String = "flow_diagram.html"
+HTMLTables.write(html_path, df)
+html_df::DataFrame = HTMLTables.read(html_path, DataFrame)
+
+println(html_df)
+
+# export the data as a Excel spreadsheet to edit then read it back to a DataFrame
+xlsx_path::String = "flow_diagram.xlsx"
+sheetname::String = "flow_diagram"
+XLSX.writetable(xlsx_path, sheetname => df)
+xlsx_df::DataFrame = DataFrame(XLSX.readtable(xlsx_path, sheetname))
+
+println(xlsx_df)
+```
+
+The updated `DataFrames` either it be from a `.csv`, `.html`, `.json`, or `.xlsx` can be loaded into the `flow_diagram` function to create the `FlowDiagram` object which can be plotted using the `Base.show`, and `Base.Multimedia.display` function. The `Base.Multimedia.display` defaults to plotting the `FlowDiagram` as a `SVG` and uses the Julia plotting plane if using VSCode. The format that `Base.show` returns is depended on the mime type represented as `Mime` in Julia. `Base.show` can use an mime type that Graphviz supports through the `Graphviz_jll` binary. The `text/vnd.graphviz` and `text/plain` mimes prints the `.gv` to `IO`:
+
+```julia
+using PRISMA: FlowDiagram, flow_diagram
+
+fd::FlowDiagram = flow_diagram()
+
+show(stdout, "text/vnd.graphviz", fd)
+show(stdout, "text/plain", fd)
+show(stdout, "application/pdf", fd)
+show(stdout, "image/png", fd)
+show(stdout, "image/svg+xml", fd)
+
+display(fd)
+```
+
+The `FlowDiagram` can be saved as any format support by `Graphviz_jll` using the `flow_diagram_save` the only catch is the file path should end with the extension of the desired format:
+
+```julia
+using PRISMA: FlowDiagram, flow_diagram
+
+fd::FlowDiagram = flow_diagram()
+
+# saves that flow diagram as an SVG
+flow_diagram_save("flow_diagram.svg", fd)
+
+# saves that flow diagram as a PNG
+flow_diagram_save("flow_diagram.png", fd)
+```
+
+The look of the `FlowDiagram` can be edited assigning new values to each of the following keyword arguments of the `flow_diagram` function: `arrow_color`, `arrow_head`, `arrow_size`, `arrow_width`, `background_color`, `border_color`, `border_style`, `border_width`, `borders`, `font`, `font_color`, `font_size`, `grayboxes`, `grayboxes_color`, `other_methods`, `previous_studies`, `side_boxes`, `side_boxes_borders`, `side_boxes_color`, `top_boxes`, `top_boxes_borders`, `top_boxes_color`. The amount of arguments allows for the `FlowDiagram` to be high customizable and variable:
+
+```julia
+using PRISMA: FlowDiagram, flow_diagram, flow_diagram_save
+
+# flow diagram with default styling
+example_01::FlowDiagram = flow_diagram()
+
+# flow diagram with custom styling
+example_02::FlowDiagram = flow_diagram(
+    arrow_color="#111111",
+    arrow_head="Vee",
+    arrow_width=2,
+    border_color="#111111",
+    border_width=2,
+    font="Helvetica",
+    font_color="#111111",
+    font_size=10,
+    grayboxes=false,
+    previous_studies=false,
+    side_boxes_borders=true,
+    side_boxes_color="white",
+    top_boxes_borders=true,
+    top_boxes_color="white"
+)
+
+flow_diagram_save("example_01.svg", example_01)
+flow_diagram_save("example_02.svg", example_02)
+
+```
+
+The flow diagram with default styling:
+
+![flow diagram with default styling](docs/src/assets/figure.svg)
+
+The flow diagram with custom styling:
+
+![flow diagram with custom styling](docs/src/assets/figure.svg)
 
 Creating a completed checklist from a paper and saving the results to a spreadsheet:
 
@@ -56,7 +168,7 @@ clist_template::DataFrame = checklist_df()
 
 println(clist_template)
 
-writetable("PRISMA_checklist.csv", "sheet_1" => clist_template)
+writetable("PRISMA_checklist.xlsx", "sheet_1" => clist_template)
 ```
 
 The `DataFrame` that is created from the `checklist_df` function can also be edited within a Julia program using functions from the `DataFrames` package:

app/frontend/src/assets/css/header.css

@@ -7,7 +7,6 @@ header {
   font-size: .85rem;
   top: 0;
   z-index: 1;
-  color: var(--text-color-1);
   background-color: var(--background-color-1);
   width: 100%;
   padding: 0 1%;