Commit ⋅ jinseob2kim/jsmodule

1	+	#' @title lineUI: shiny module UI for lineplot
2	+	#' @description Shiny module UI for lineplot
3	+	#' @param id id
4	+	#' @param label label
5	+	#' @return Shiny module UI for lineplot
6	+	#' @details Shiny module UI for lineplot
7	+	#' @examples
8	+	#' library(shiny);library(ggplot2);library(ggpubr);
9	+	#' ui <- fluidPage(
10	+	#' sidebarLayout(
11	+	#' sidebarPanel(
12	+	#' lineUI("line")
13	+	#' ),
14	+	#' mainPanel(
15	+	#' plotOutput("line_plot"),
16	+	#' ggplotdownUI("line")
17	+	#' )
18	+	#' )
19	+	#')
20	+	#'
21	+	#' server <- function(input, output, session) {
22	+	#'
23	+	#' data <- reactive(mtcars)
24	+	#' data.label <- reactive(jstable::mk.lev(mtcars))
25	+	#'
26	+	#' out_line <- lineServer("line", data = data, data_label = data.label,
27	+	#' data_varStruct = NULL)
28	+	#'
29	+	#' output$line_plot <- renderPlot({
30	+	#' print(out_line())
31	+	#' })
32	+	#'}
33	+	#' @rdname lineUI
34	+	#' @export
35	+
36	+
37	+	lineUI <- function(id, label = "lineplot") {
38	+	# Create a namespace function using the provided id
39	+	ns <- NS(id)
40	+
41	+	tagList(
42	+	uiOutput(ns("vars_line")),
43	+	uiOutput(ns("strata_line")),
44	+	radioButtons(ns("options"), "Option", choices = c("Mean_SE", "Mean_SD", "Median_IQR"), selected = "Mean_SE", inline = T),
45	+	checkboxInput(ns("linetype"), "Linetype"),
46	+	checkboxInput(ns("jitter"), "Jitter"),
47	+	uiOutput(ns("subvar")),
48	+	uiOutput(ns("subval"))
49	+
50	+	)
51	+	}
52	+
53	+
54	+	#' @title lineServer: shiny module server for lineplot.
55	+	#' @description Shiny module server for lineplot.
56	+	#' @param id id
57	+	#' @param data Reactive data
58	+	#' @param data_label Reactive data label
59	+	#' @param data_varStruct Reactive List of variable structure, Default: NULL
60	+	#' @param nfactor.limit nlevels limit in factor variable, Default: 10
61	+	#' @return Shiny module server for lineplot.
62	+	#' @details Shiny module server for lineplot.
63	+	#' @examples
64	+	#' library(shiny);library(ggplot2);library(ggpubr);
65	+	#' ui <- fluidPage(
66	+	#' sidebarLayout(
67	+	#' sidebarPanel(
68	+	#' lineUI("line")
69	+	#' ),
70	+	#' mainPanel(
71	+	#' plotOutput("line_plot"),
72	+	#' ggplotdownUI("line")
73	+	#' )
74	+	#' )
75	+	#')
76	+	#'
77	+	#' server <- function(input, output, session) {
78	+	#'
79	+	#' data <- reactive(mtcars)
80	+	#' data.label <- reactive(jstable::mk.lev(mtcars))
81	+	#'
82	+	#' out_line <- lineServer("line", data = data, data_label = data.label,
83	+	#' data_varStruct = NULL)
84	+	#'
85	+	#' output$line_plot <- renderPlot({
86	+	#' print(out_line())
87	+	#' })
88	+	#'}
89	+	#' @rdname lineServer
90	+	#' @export
91	+	#' @import shiny
92	+	#' @importFrom data.table data.table .SD :=
93	+	#' @importFrom ggpubr ggline
94	+	#' @importFrom ggplot2 ggsave
95	+	#' @importFrom rvg dml
96	+	#' @importFrom officer read_pptx add_slide ph_with ph_location
97	+
98	+
99	+
100	+	lineServer <- function(id, data, data_label, data_varStruct = NULL, nfactor.limit = 10) {
101	+	moduleServer(id,
102	+	function(input, output, session) {
103	+	## To remove NOTE.
104	+	level <- val_label <- variable <- NULL
105	+
106	+	if (is.null(data_varStruct)){
107	+	data_varStruct = reactive(list(variable = names(data())))
108	+	}
109	+
110	+
111	+	vlist <- reactive({
112	+
113	+	data <- data.table(data(), stringsAsFactors = T)
114	+
115	+	factor_vars <- names(data)[data[, lapply(.SD, class) %in% c("factor", "character")]]
116	+	#data[, (factor_vars) := lapply(.SD, as.factor), .SDcols= factor_vars]
117	+	factor_list <- mklist(data_varStruct(), factor_vars)
118	+
119	+	nclass_factor <- unlist(data[, lapply(.SD, function(x){length(levels(x))}), .SDcols = factor_vars])
120	+
121	+	group_vars <- factor_vars[nclass_factor >=2 & nclass_factor <= nfactor.limit & nclass_factor < nrow(data)]
122	+	group_list <- mklist(data_varStruct(), group_vars)
123	+
124	+	except_vars <- factor_vars[nclass_factor > nfactor.limit \| nclass_factor == 1 \| nclass_factor == nrow(data)]
125	+
126	+	select_vars <- setdiff(names(data), factor_vars)
127	+	select_list <- mklist(data_varStruct(), select_vars)
128	+
129	+	return(list(factor_vars = factor_vars, factor_list = factor_list, nclass_factor = nclass_factor, group_vars = group_vars, group_list = group_list, except_vars = except_vars,
130	+	select_vars = select_vars, select_list = select_list))
131	+	})
132	+
133	+	output$vars_line <- renderUI({
134	+	tagList(
135	+	selectizeInput(session$ns("x_line"), "X variable",
136	+	choices = vlist()$factor_vars, multiple = F,
137	+	selected = vlist()$select_vars[1]
138	+	),
139	+	selectizeInput(session$ns("y_line"), "Y variable",
140	+	choices = vlist()$select_list, multiple = F,
141	+	selected = ifelse(length(vlist()$select_vars) > 1, vlist()$select_vars[2], vlist()$select_vars[1])
142	+	)
143	+	)
144	+
145	+	})
146	+
147	+	output$strata_line <- renderUI({
148	+	strata_vars <- setdiff(vlist()$factor_vars, vlist()$except_vars)
149	+	strata_vars <- setdiff(strata_vars, input$x_line)
150	+	strata_list <- mklist(data_varStruct(), strata_vars)
151	+	strata_select <- c("None", strata_list)
152	+	selectizeInput(session$ns("strata"), "Strata",
153	+	choices = strata_select, multiple = F,
154	+	selected = unlist(strata_select)[1]
155	+	)
156	+
157	+	})
158	+
159	+
160	+	observeEvent(input$subcheck, {
161	+	output$subvar <- renderUI({
162	+	req(input$subcheck == T)
163	+	req(!is.null(input$x_line))
164	+
165	+	var_subgroup <- setdiff(names(data()), c(vlist()$except_vars, input$x_line, input$y_line, input$strata))
166	+
167	+	var_subgroup_list <- mklist(data_varStruct(), var_subgroup)
168	+	validate(
169	+	need(length(var_subgroup) > 0 , "No variables for sub-group analysis")
170	+	)
171	+
172	+	tagList(
173	+	selectInput(session$ns("subvar_km"), "Sub-group variables",
174	+	choices = var_subgroup_list, multiple = T,
175	+	selected = var_subgroup[1])
176	+	)
177	+
178	+
179	+	})
180	+
181	+	})
182	+
183	+
184	+	output$subval <- renderUI({
185	+	req(input$subcheck == T)
186	+	req(length(input$subvar_km) > 0)
187	+
188	+	outUI <- tagList()
189	+
190	+	for (v in seq_along(input$subvar_km)){
191	+	if (input$subvar_km[[v]] %in% vlist()$factor_vars){
192	+	outUI[[v]] <- selectInput(session$ns(paste0("subval_km", v)), paste0("Sub-group value: ", input$subvar_km[[v]]),
193	+	choices = data_label()[variable == input$subvar_km[[v]], level], multiple = T,
194	+	selected = data_label()[variable == input$subvar_km[[v]], level][1])
195	+	} else{
196	+	val <- stats::quantile(data()[[input$subvar_km[[v]]]], na.rm = T)
197	+	outUI[[v]] <- sliderInput(session$ns(paste0("subval_km", v)), paste0("Sub-group range: ", input$subvar_km[[v]]),
198	+	min = val[1], max = val[5],
199	+	value = c(val[2], val[4]))
200	+	}
201	+
202	+	}
203	+	outUI
204	+
205	+	})
206	+
207	+	lineInput <- reactive({
208	+	req(c(input$x_line, input$y_line, input$strata))
209	+	data <- data.table(data())
210	+	label <- data_label()
211	+	add <- switch(input$options,
212	+	"Mean_SE" = "mean_se",
213	+	"Mean_SD" = "mean_sd",
214	+	"Median_IQR" = "median_iqr"
215	+	)
216	+	if(input$jitter){
217	+	add <- switch(input$options,
218	+	"Mean_SE" = c("jitter", "mean_se"),
219	+	"Mean_SD" = c("jitter","mean_sd"),
220	+	"Median_IQR" = c("jitter", "median_iqr")
221	+	)
222	+	}
223	+
224	+
225	+	color <- ifelse(input$strata == "None", "black", input$strata)
226	+	fill <- ifelse(input$strata=="None", input$x_line , input$strata)
227	+	if (input$strata != "None"){
228	+	data <- data[!is.na(get(input$strata))]
229	+	}
230	+	add.params <- list()
231	+	cor.coeff.args <- list(p.accuracy = 0.001)
232	+
233	+
234	+
235	+	linetype = 19
236	+	if (input$linetype){
237	+	if(input$strata == "None"){
238	+	linetype = 20
239	+	} else {
240	+	linetype <- input$strata
241	+	}
242	+
243	+	}
244	+
245	+
246	+	ggpubr::ggline(data, input$x_line, input$y_line, color = color, add = add, add.params = add.params, conf.int = input$lineci,
247	+	xlab = label[variable == input$x_line, var_label][1],
248	+	ylab = label[variable == input$y_line, var_label][1], na.rm = T,
249	+	linetype = linetype
250	+	)
251	+	})
252	+
253	+	output$downloadControls <- renderUI({
254	+	tagList(
255	+	column(4,
256	+	selectizeInput(session$ns("file_ext"), "File extension (dpi = 300)",
257	+	choices = c("jpg","pdf", "tiff", "svg", "pptx"), multiple = F,
258	+	selected = "pptx"
259	+	)
260	+	),
261	+	column(4,
262	+	sliderInput(session$ns("fig_width"), "Width (in):",
263	+	min = 5, max = 15, value = 8
264	+	)
265	+	),
266	+	column(4,
267	+	sliderInput(session$ns("fig_height"), "Height (in):",
268	+	min = 5, max = 15, value = 6
269	+	)
270	+	)
271	+	)
272	+	})
273	+
274	+	output$downloadButton <- downloadHandler(
275	+	filename = function() {
276	+	paste(input$x_line, "_", input$y_line,"_lineplot.",input$file_ext ,sep="")
277	+
278	+	},
279	+	# content is a function with argument file. content writes the plot to the device
280	+	content = function(file) {
281	+	withProgress(message = 'Download in progress',
282	+	detail = 'This may take a while...', value = 0, {
283	+	for (i in 1:15) {
284	+	incProgress(1/15)
285	+	Sys.sleep(0.01)
286	+	}
287	+
288	+	if (input$file_ext == "pptx"){
289	+	my_vec_graph <- rvg::dml(ggobj = lineInput())
290	+
291	+	doc <- officer::read_pptx()
292	+	doc <- officer::add_slide(doc, layout = "Title and Content", master = "Office Theme")
293	+	doc <- officer::ph_with(doc, my_vec_graph, location = officer::ph_location(width = input$fig_width, height = input$fig_height))
294	+	print(doc, target = file)
295	+
296	+	} else{
297	+	ggplot2::ggsave(file, lineInput(), dpi = 300, units = "in", width = input$fig_width, height =input$fig_height)
298	+	}
299	+	})
300	+
301	+	}
302	+	)
303	+
304	+	return(lineInput)
305	+
306	+
307	+
308	+
309	+
310	+	}
311	+	)
312	+
313	+
314	+
315	+
316	+
317	+
318	+
319	+
320	+
321	+
322	+
323	+
324	+
325	+
326	+
327	+
328	+
329	+
330	+	}
331	+	#####
332	+
333	+
334	+
335	+
336	+	# ui <- fluidPage(
337	+	# sidebarLayout(
338	+	# sidebarPanel(
339	+	# lineUI("line")
340	+	# ),
341	+	# mainPanel(
342	+	# plotOutput("line_plot"),
343	+	# ggplotdownUI("line")
344	+	# )
345	+	# )
346	+	# )
347	+	#
348	+	# server <- function(input, output, session) {
349	+	# mtcars$am <- as.factor(mtcars$am)
350	+	# mtcars$vs <- as.factor(mtcars$vs)
351	+	# mtcars$gear <- as.factor(mtcars$gear)
352	+	# mtcars$carb <- as.factor(mtcars$carb)
353	+	# mtcars$cyl <- as.factor(mtcars$cyl)
354	+	# data <- reactive(mtcars)
355	+	# data.label <- reactive(jstable::mk.lev(mtcars))
356	+	# out_line <- lineServer("line", data = data, data_label = data.label,
357	+	# data_varStruct = NULL)
358	+	#
359	+	# output$line_plot <- renderPlot({
360	+	# print(out_line())
361	+	# })
362	+	# }
363	+	#
364	+	# shinyApp(ui, server)

@@ -0,0 +1,382 @@

1	+	#' @title boxUI: shiny module UI for boxplot
2	+	#' @description Shiny module UI for boxplot
3	+	#' @param id id
4	+	#' @param label label
5	+	#' @return Shiny module UI for boxplot
6	+	#' @details Shiny module UI for boxplot
7	+	#' @examples
8	+	#' library(shiny);library(ggplot2);library(ggpubr);
9	+	#' ui <- fluidPage(
10	+	#' sidebarLayout(
11	+	#' sidebarPanel(
12	+	#' boxUI("box")
13	+	#' ),
14	+	#' mainPanel(
15	+	#' plotOutput("box_plot"),
16	+	#' ggplotdownUI("box")
17	+	#' )
18	+	#' )
19	+	#')
20	+	#'
21	+	#' server <- function(input, output, session) {
22	+	#'
23	+	#' data <- reactive(mtcars)
24	+	#' data.label <- reactive(jstable::mk.lev(mtcars))
25	+	#'
26	+	#' out_box <- boxServer("box", data = data, data_label = data.label,
27	+	#' data_varStruct = NULL)
28	+	#'
29	+	#' output$box_plot <- renderPlot({
30	+	#' print(out_box())
31	+	#' })
32	+	#'}
33	+	#' @rdname boxUI
34	+	#' @export
35	+
36	+
37	+	boxUI <- function(id, label = "boxplot") {
38	+	# Create a namespace function using the provided id
39	+	ns <- NS(id)
40	+
41	+	tagList(
42	+	uiOutput(ns("vars_box")),
43	+	uiOutput(ns("strata_box")),
44	+	checkboxInput(ns("errorbar"), "Errorbar"),
45	+	checkboxInput(ns("jitter"), "Points"),
46	+	checkboxInput(ns("fillcolor"), "Fill"),
47	+	uiOutput(ns("subvar")),
48	+	uiOutput(ns("subval"))
49	+
50	+	)
51	+	}
52	+
53	+
54	+	#' @title boxServer: shiny module server for boxplot.
55	+	#' @description Shiny module server for boxplot.
56	+	#' @param id id
57	+	#' @param data Reactive data
58	+	#' @param data_label Reactive data label
59	+	#' @param data_varStruct Reactive List of variable structure, Default: NULL
60	+	#' @param nfactor.limit nlevels limit in factor variable, Default: 10
61	+	#' @return Shiny module server for boxplot.
62	+	#' @details Shiny module server for boxplot.
63	+	#' @examples
64	+	#' library(shiny);library(ggplot2);library(ggpubr);
65	+	#' ui <- fluidPage(
66	+	#' sidebarLayout(
67	+	#' sidebarPanel(
68	+	#' boxUI("box")
69	+	#' ),
70	+	#' mainPanel(
71	+	#' plotOutput("box_plot"),
72	+	#' ggplotdownUI("box")
73	+	#' )
74	+	#' )
75	+	#')
76	+	#'
77	+	#' server <- function(input, output, session) {
78	+	#'
79	+	#' data <- reactive(mtcars)
80	+	#' data.label <- reactive(jstable::mk.lev(mtcars))
81	+	#'
82	+	#' out_box <- boxServer("box", data = data, data_label = data.label,
83	+	#' data_varStruct = NULL)
84	+	#'
85	+	#' output$box_plot <- renderPlot({
86	+	#' print(out_box())
87	+	#' })
88	+	#'}
89	+	#' @rdname boxServer
90	+	#' @export
91	+	#' @import shiny
92	+	#' @importFrom data.table data.table .SD :=
93	+	#' @importFrom ggpubr ggboxplot
94	+	#' @importFrom ggplot2 ggsave
95	+	#' @importFrom rvg dml
96	+	#' @importFrom officer read_pptx add_slide ph_with ph_location
97	+
98	+
99	+
100	+	boxServer <- function(id, data, data_label, data_varStruct = NULL, nfactor.limit = 10) {
101	+	moduleServer(id,
102	+	function(input, output, session) {
103	+	## To remove NOTE.
104	+	level <- val_label <- variable <- NULL
105	+
106	+	if (is.null(data_varStruct)){
107	+	data_varStruct = reactive(list(variable = names(data())))
108	+	}
109	+
110	+
111	+	vlist <- reactive({
112	+
113	+	data <- data.table(data(), stringsAsFactors = T)
114	+
115	+	factor_vars <- names(data)[data[, lapply(.SD, class) %in% c("factor", "character")]]
116	+	#data[, (factor_vars) := lapply(.SD, as.factor), .SDcols= factor_vars]
117	+	factor_list <- mklist(data_varStruct(), factor_vars)
118	+
119	+	nclass_factor <- unlist(data[, lapply(.SD, function(x){length(levels(x))}), .SDcols = factor_vars])
120	+
121	+	group_vars <- factor_vars[nclass_factor >=2 & nclass_factor <= nfactor.limit & nclass_factor < nrow(data)]
122	+	group_list <- mklist(data_varStruct(), group_vars)
123	+
124	+	except_vars <- factor_vars[nclass_factor > nfactor.limit \| nclass_factor == 1 \| nclass_factor == nrow(data)]
125	+
126	+	select_vars <- setdiff(names(data), factor_vars)
127	+	select_list <- mklist(data_varStruct(), select_vars)
128	+
129	+	return(list(factor_vars = factor_vars, factor_list = factor_list, nclass_factor = nclass_factor, group_vars = group_vars, group_list = group_list, except_vars = except_vars,
130	+	select_vars = select_vars, select_list = select_list))
131	+	})
132	+
133	+	output$vars_box <- renderUI({
134	+	tagList(
135	+	selectizeInput(session$ns("x_box"), "X variable",
136	+	choices = vlist()$factor_vars, multiple = F,
137	+	selected = vlist()$select_vars[1]
138	+	),
139	+	selectizeInput(session$ns("y_box"), "Y variable",
140	+	choices = vlist()$select_list, multiple = F,
141	+	selected = ifelse(length(vlist()$select_vars) > 1, vlist()$select_vars[2], vlist()$select_vars[1])
142	+	)
143	+	)
144	+
145	+	})
146	+
147	+	output$strata_box <- renderUI({
148	+	strata_vars <- setdiff(vlist()$factor_vars, vlist()$except_vars)
149	+	strata_vars <- setdiff(strata_vars, input$x_box)
150	+	strata_list <- mklist(data_varStruct(), strata_vars)
151	+	strata_select <- c("None", strata_list)
152	+	selectizeInput(session$ns("strata"), "Strata",
153	+	choices = strata_select, multiple = F,
154	+	selected = unlist(strata_select)[1]
155	+	)
156	+
157	+	})
158	+
159	+
160	+	observeEvent(input$subcheck, {
161	+	output$subvar <- renderUI({
162	+	req(input$subcheck == T)
163	+	req(!is.null(input$x_box))
164	+
165	+	var_subgroup <- setdiff(names(data()), c(vlist()$except_vars, input$x_box, input$y_box, input$strata))
166	+
167	+	var_subgroup_list <- mklist(data_varStruct(), var_subgroup)
168	+	validate(
169	+	need(length(var_subgroup) > 0 , "No variables for sub-group analysis")
170	+	)
171	+
172	+	tagList(
173	+	selectInput(session$ns("subvar_km"), "Sub-group variables",
174	+	choices = var_subgroup_list, multiple = T,
175	+	selected = var_subgroup[1])
176	+	)
177	+
178	+
179	+	})
180	+
181	+	})
182	+
183	+
184	+	output$subval <- renderUI({
185	+	req(input$subcheck == T)
186	+	req(length(input$subvar_km) > 0)
187	+
188	+	outUI <- tagList()
189	+
190	+	for (v in seq_along(input$subvar_km)){
191	+	if (input$subvar_km[[v]] %in% vlist()$factor_vars){
192	+	outUI[[v]] <- selectInput(session$ns(paste0("subval_km", v)), paste0("Sub-group value: ", input$subvar_km[[v]]),
193	+	choices = data_label()[variable == input$subvar_km[[v]], level], multiple = T,
194	+	selected = data_label()[variable == input$subvar_km[[v]], level][1])
195	+	} else{
196	+	val <- stats::quantile(data()[[input$subvar_km[[v]]]], na.rm = T)
197	+	outUI[[v]] <- sliderInput(session$ns(paste0("subval_km", v)), paste0("Sub-group range: ", input$subvar_km[[v]]),
198	+	min = val[1], max = val[5],
199	+	value = c(val[2], val[4]))
200	+	}
201	+
202	+	}
203	+	outUI
204	+
205	+	})
206	+
207	+	boxInput <- reactive({
208	+	req(c(input$x_box, input$y_box, input$strata))
209	+	data <- data.table(data())
210	+	label <- data_label()
211	+	color <- ifelse(input$strata == "None", input$x_box, input$strata)
212	+	fill <- ifelse(input$strata=="None", input$x_box , input$strata)
213	+	if (input$strata != "None"){
214	+	data <- data[!is.na(get(input$strata))]
215	+	}
216	+	add.params <- list()
217	+	cor.coeff.args <- list(p.accuracy = 0.001)
218	+
219	+	add ="none"
220	+	if (input$jitter){
221	+	add <- "jitter"
222	+	}
223	+
224	+	fillcolor ="white"
225	+	if (input$fillcolor){
226	+	fillcolor <-"gray"
227	+	}
228	+
229	+	ggpubr::ggboxplot(data, input$x_box, input$y_box, color = color, add = add, add.params = add.params, conf.int = input$lineci,
230	+	xlab = label[variable == input$x_box, var_label][1],
231	+	ylab = label[variable == input$y_box, var_label][1], na.rm = T, fill=fillcolor, error.plot = "errorbar",
232	+	bxp.errorbar = input$errorbar
233	+	)
234	+	})
235	+
236	+	output$downloadControls <- renderUI({
237	+	tagList(
238	+	column(4,
239	+	selectizeInput(session$ns("file_ext"), "File extension (dpi = 300)",
240	+	choices = c("jpg","pdf", "tiff", "svg", "pptx"), multiple = F,
241	+	selected = "pptx"
242	+	)
243	+	),
244	+	column(4,
245	+	sliderInput(session$ns("fig_width"), "Width (in):",
246	+	min = 5, max = 15, value = 8
247	+	)
248	+	),
249	+	column(4,
250	+	sliderInput(session$ns("fig_height"), "Height (in):",
251	+	min = 5, max = 15, value = 6
252	+	)
253	+	)
254	+	)
255	+	})
256	+
257	+	output$downloadButton <- downloadHandler(
258	+	filename = function() {
259	+	paste(input$x_box, "_", input$y_box,"_boxplot.",input$file_ext ,sep="")
260	+
261	+	},
262	+	# content is a function with argument file. content writes the plot to the device
263	+	content = function(file) {
264	+	withProgress(message = 'Download in progress',
265	+	detail = 'This may take a while...', value = 0, {
266	+	for (i in 1:15) {
267	+	incProgress(1/15)
268	+	Sys.sleep(0.01)
269	+	}
270	+
271	+	if (input$file_ext == "pptx"){
272	+	my_vec_graph <- rvg::dml(ggobj = boxInput())
273	+
274	+	doc <- officer::read_pptx()
275	+	doc <- officer::add_slide(doc, layout = "Title and Content", master = "Office Theme")
276	+	doc <- officer::ph_with(doc, my_vec_graph, location = officer::ph_location(width = input$fig_width, height = input$fig_height))
277	+	print(doc, target = file)
278	+
279	+	} else{
280	+	ggplot2::ggsave(file, boxInput(), dpi = 300, units = "in", width = input$fig_width, height =input$fig_height)
281	+	}
282	+	})
283	+
284	+	}
285	+	)
286	+
287	+	return(boxInput)
288	+
289	+
290	+
291	+
292	+
293	+	}
294	+	)
295	+
296	+
297	+
298	+
299	+
300	+
301	+
302	+
303	+
304	+
305	+
306	+
307	+
308	+
309	+
310	+
311	+
312	+
313	+	}
314	+	#####
315	+
316	+
317	+	#
318	+	# ui <- navbarPage("basic statistics",
319	+	# navbarMenu("Plot", icon = icon("bar-chart-o"),
320	+	# tabPanel("Boxplot",
321	+	# sidebarLayout(
322	+	# sidebarPanel(
323	+	# boxUI("box")
324	+	# ),
325	+	# mainPanel(
326	+	# withLoader(plotOutput("box_plot"), type="html", loader="loader6"),
327	+	# ggplotdownUI("box")
328	+	# )
329	+	# )
330	+	# )
331	+	# )
332	+	# )
333	+	#
334	+	# server <- function(input, output, session){
335	+	#
336	+	# data <- reactive(mtcars)
337	+	# data.label <- reactive(jstable::mk.lev(mtcars))
338	+	# out_box <- boxServer("box", data = data, data_label = data.label, data_varStruct = NULL, nfactor.limit = 20)
339	+	#
340	+	# output$box_plot <- renderPlot({
341	+	# print(out_box())
342	+	#
343	+	#
344	+	# output$box_plot <- renderPlot({
345	+	# # print(out_box())
346	+	# })
347	+	# }
348	+	#
349	+	# shinyApp(ui, server)
350	+
351	+	#
352	+	#
353	+	# ui <- fluidPage(
354	+	# sidebarLayout(
355	+	# sidebarPanel(
356	+	# boxUI("box")
357	+	# ),
358	+	# mainPanel(
359	+	# plotOutput("box_plot"),
360	+	# ggplotdownUI("box")
361	+	# )
362	+	# )
363	+	# )
364	+	#
365	+	# server <- function(input, output, session) {
366	+	# mtcars$am <- as.factor(mtcars$am)
367	+	# mtcars$vs <- as.factor(mtcars$vs)
368	+	# mtcars$gear <- as.factor(mtcars$gear)
369	+	# mtcars$carb <- as.factor(mtcars$carb)
370	+	# mtcars$cyl <- as.factor(mtcars$cyl)
371	+	# data <- reactive(mtcars)
372	+	# data.label <- reactive(jstable::mk.lev(mtcars))
373	+	# out_box <- boxServer("box", data = data, data_label = data.label,
374	+	# data_varStruct = NULL)
375	+	#
376	+	# output$box_plot <- renderPlot({
377	+	# print(out_box())
378	+	# })
379	+	# }
380	+	#
381	+	# shinyApp(ui, server)
382	+

@@ -142,6 +142,39 @@

142	142		)
143	143		)
144	144		),
	145	+	tabPanel("Boxplot",
	146	+	sidebarLayout(
	147	+	sidebarPanel(
	148	+	boxUI("box")
	149	+	),
	150	+	mainPanel(
	151	+	withLoader(plotOutput("box_plot"), type="html", loader="loader6"),
	152	+	ggplotdownUI("box")
	153	+	)
	154	+	)
	155	+	),
	156	+	tabPanel("Barplot",
	157	+	sidebarLayout(
	158	+	sidebarPanel(
	159	+	barUI("bar")
	160	+	),
	161	+	mainPanel(
	162	+	withLoader(plotOutput("bar_plot"), type="html", loader="loader6"),
	163	+	ggplotdownUI("bar")
	164	+	)
	165	+	)
	166	+	),
	167	+	tabPanel("Lineplot",
	168	+	sidebarLayout(
	169	+	sidebarPanel(
	170	+	lineUI("line")
	171	+	),
	172	+	mainPanel(
	173	+	withLoader(plotOutput("line_plot"), type="html", loader="loader6"),
	174	+	ggplotdownUI("line")
	175	+	)
	176	+	)
	177	+	),
145	178		tabPanel("Kaplan-meier plot",
146	179		sidebarLayout(
147	180		sidebarPanel(

@@ -423,11 +456,11 @@

      tb <- out_tb1()$table
      cap <- out_tb1()$caption
      out.tb1 <- datatable(tb, rownames = T, extensions = "Buttons", caption = cap,
                          options = c(jstable::opt.tb1("tb1"),
                                      list(columnDefs = list(list(visible=FALSE, targets= which(colnames(tb) %in% c("test","sig"))))
                                      ),
                                      list(scrollX = TRUE)
                          )
                           options = c(jstable::opt.tb1("tb1"),
                                       list(columnDefs = list(list(visible=FALSE, targets= which(colnames(tb) %in% c("test","sig"))))
                                       ),
                                       list(scrollX = TRUE)
                           )
      )
      if ("sig" %in% colnames(tb)){
        out.tb1 = out.tb1 %>% formatStyle("sig", target = 'row' ,backgroundColor = styleEqual("**", 'yellow'))

@@ -490,6 +523,24 @@

      print(out_scatter())
    })

    out_box <- boxServer("box", data = data, data_label = data.label, data_varStruct = NULL, nfactor.limit = nfactor.limit)

    output$box_plot <- renderPlot({
      print(out_box())
    })

    out_bar <- barServer("bar", data = data, data_label = data.label, data_varStruct = NULL, nfactor.limit = nfactor.limit)

    output$bar_plot <- renderPlot({
      print(out_bar())
    })

    out_line <- lineServer("line", data = data, data_label = data.label, data_varStruct = NULL, nfactor.limit = nfactor.limit)

    output$line_plot <- renderPlot({
      print(out_line())
    })

    out_kaplan <- callModule(kaplanModule, "kaplan", data = data, data_label = data.label, data_varStruct = NULL, nfactor.limit = nfactor.limit)

    output$kaplan_plot <- renderPlot({

@@ -684,6 +735,39 @@

684	735		)
685	736		)
686	737		),
	738	+	tabPanel("Boxplot",
	739	+	sidebarLayout(
	740	+	sidebarPanel(
	741	+	boxUI("box")
	742	+	),
	743	+	mainPanel(
	744	+	withLoader(plotOutput("box_plot"), type="html", loader="loader6"),
	745	+	ggplotdownUI("box")
	746	+	)
	747	+	)
	748	+	),
	749	+	tabPanel("Barplot",
	750	+	sidebarLayout(
	751	+	sidebarPanel(
	752	+	barUI("bar")
	753	+	),
	754	+	mainPanel(
	755	+	withLoader(plotOutput("bar_plot"), type="html", loader="loader6"),
	756	+	ggplotdownUI("bar")
	757	+	)
	758	+	)
	759	+	),
	760	+	tabPanel("Lineplot",
	761	+	sidebarLayout(
	762	+	sidebarPanel(
	763	+	lineUI("line")
	764	+	),
	765	+	mainPanel(
	766	+	withLoader(plotOutput("line_plot"), type="html", loader="loader6"),
	767	+	ggplotdownUI("line")
	768	+	)
	769	+	)
	770	+	),
687	771		tabPanel("Kaplan-meier plot",
688	772		sidebarLayout(
689	773		sidebarPanel(

@@ -844,6 +928,25 @@

      print(out_scatter())
    })

    out_box <- boxServer("box", data = data, data_label = data.label, data_varStruct = NULL, nfactor.limit = nfactor.limit)

    output$box_plot <- renderPlot({
      print(out_box())
    })

    out_bar <- barServer("bar", data = data, data_label = data.label, data_varStruct = NULL, nfactor.limit = nfactor.limit)

    output$bar_plot <- renderPlot({
      print(out_bar())
    })

    out_line <- lineServer("line", data = data, data_label = data.label, data_varStruct = NULL, nfactor.limit = nfactor.limit)

    output$line_plot <- renderPlot({
      print(out_line())
    })


    out_kaplan <- callModule(kaplanModule, "kaplan", data = data, data_label = data.label, data_varStruct = NULL, nfactor.limit = nfactor.limit)

    output$kaplan_plot <- renderPlot({

@@ -0,0 +1,356 @@

1	+	#' @title barUI: shiny module UI for barplot
2	+	#' @description Shiny module UI for barplot
3	+	#' @param id id
4	+	#' @param label label
5	+	#' @return Shiny module UI for barplot
6	+	#' @details Shiny module UI for barplot
7	+	#' @examples
8	+	#' library(shiny);library(ggplot2);library(ggpubr);
9	+	#' ui <- fluidPage(
10	+	#' sidebarLayout(
11	+	#' sidebarPanel(
12	+	#' barUI("bar")
13	+	#' ),
14	+	#' mainPanel(
15	+	#' plotOutput("bar_plot"),
16	+	#' ggplotdownUI("bar")
17	+	#' )
18	+	#' )
19	+	#')
20	+	#'
21	+	#' server <- function(input, output, session) {
22	+	#'
23	+	#' data <- reactive(mtcars)
24	+	#' data.label <- reactive(jstable::mk.lev(mtcars))
25	+	#'
26	+	#' out_bar <- barServer("bar", data = data, data_label = data.label,
27	+	#' data_varStruct = NULL)
28	+	#'
29	+	#' output$bar_plot <- renderPlot({
30	+	#' print(out_bar())
31	+	#' })
32	+	#'}
33	+	#' @rdname barUI
34	+	#' @export
35	+
36	+
37	+
38	+	barUI <- function(id, label = "barplot") {
39	+	# Create a namespace function using the provided id
40	+	ns <- NS(id)
41	+
42	+	tagList(
43	+	uiOutput(ns("vars_bar")),
44	+	uiOutput(ns("strata_bar")),
45	+	checkboxInput(ns("fill"), "Fill"),
46	+	checkboxInput(ns("mean"), "Mean_SE"),
47	+	checkboxInput(ns("jitter"), "Jitter"),
48	+	uiOutput(ns("subvar")),
49	+	uiOutput(ns("subval"))
50	+
51	+	)
52	+	}
53	+
54	+
55	+	#' @title barServer: shiny module server for barplot.
56	+	#' @description Shiny module server for barplot.
57	+	#' @param id id
58	+	#' @param data Reactive data
59	+	#' @param data_label Reactive data label
60	+	#' @param data_varStruct Reactive List of variable structure, Default: NULL
61	+	#' @param nfactor.limit nlevels limit in factor variable, Default: 10
62	+	#' @return Shiny module server for barplot.
63	+	#' @details Shiny module server for barplot.
64	+	#' @examples
65	+	#' library(shiny);library(ggplot2);library(ggpubr);
66	+	#' ui <- fluidPage(
67	+	#' sidebarLayout(
68	+	#' sidebarPanel(
69	+	#' barUI("bar")
70	+	#' ),
71	+	#' mainPanel(
72	+	#' plotOutput("bar_plot"),
73	+	#' ggplotdownUI("bar")
74	+	#' )
75	+	#' )
76	+	#')
77	+	#'
78	+	#' server <- function(input, output, session) {
79	+	#'
80	+	#' data <- reactive(mtcars)
81	+	#' data.label <- reactive(jstable::mk.lev(mtcars))
82	+	#'
83	+	#' out_bar <- barServer("bar", data = data, data_label = data.label,
84	+	#' data_varStruct = NULL)
85	+	#'
86	+	#' output$bar_plot <- renderPlot({
87	+	#' print(out_bar())
88	+	#' })
89	+	#'}
90	+	#' @rdname barServer
91	+	#' @export
92	+	#' @import shiny
93	+	#' @importFrom data.table data.table .SD :=
94	+	#' @importFrom ggpubr ggbarplot
95	+	#' @importFrom ggplot2 ggsave
96	+	#' @importFrom rvg dml
97	+	#' @importFrom officer read_pptx add_slide ph_with ph_location
98	+
99	+
100	+
101	+	barServer <- function(id, data, data_label, data_varStruct = NULL, nfactor.limit = 10) {
102	+	moduleServer(id,
103	+	function(input, output, session) {
104	+	## To remove NOTE.
105	+	level <- val_label <- variable <- NULL
106	+
107	+	if (is.null(data_varStruct)){
108	+	data_varStruct = reactive(list(variable = names(data())))
109	+	}
110	+
111	+
112	+	vlist <- reactive({
113	+
114	+	data <- data.table(data(), stringsAsFactors = T)
115	+
116	+	factor_vars <- names(data)[data[, lapply(.SD, class) %in% c("factor", "character")]]
117	+	#data[, (factor_vars) := lapply(.SD, as.factor), .SDcols= factor_vars]
118	+	factor_list <- mklist(data_varStruct(), factor_vars)
119	+
120	+	nclass_factor <- unlist(data[, lapply(.SD, function(x){length(levels(x))}), .SDcols = factor_vars])
121	+
122	+	group_vars <- factor_vars[nclass_factor >=2 & nclass_factor <= nfactor.limit & nclass_factor < nrow(data)]
123	+	group_list <- mklist(data_varStruct(), group_vars)
124	+
125	+	except_vars <- factor_vars[nclass_factor > nfactor.limit \| nclass_factor == 1 \| nclass_factor == nrow(data)]
126	+
127	+	select_vars <- setdiff(names(data), factor_vars)
128	+	select_list <- mklist(data_varStruct(), select_vars)
129	+
130	+	return(list(factor_vars = factor_vars, factor_list = factor_list, nclass_factor = nclass_factor, group_vars = group_vars, group_list = group_list, except_vars = except_vars,
131	+	select_vars = select_vars, select_list = select_list))
132	+	})
133	+
134	+	output$vars_bar <- renderUI({
135	+	tagList(
136	+	selectizeInput(session$ns("x_bar"), "X variable",
137	+	choices = vlist()$factor_vars, multiple = F,
138	+	selected = vlist()$select_vars[1]
139	+	),
140	+	selectizeInput(session$ns("y_bar"), "Y variable",
141	+	choices = vlist()$select_list, multiple = F,
142	+	selected = ifelse(length(vlist()$select_vars) > 1, vlist()$select_vars[2], vlist()$select_vars[1])
143	+	)
144	+	)
145	+
146	+	})
147	+
148	+	output$strata_bar <- renderUI({
149	+	strata_vars <- setdiff(vlist()$factor_vars, vlist()$except_vars)
150	+	strata_vars <- setdiff(strata_vars, input$x_bar)
151	+	strata_list <- mklist(data_varStruct(), strata_vars)
152	+	strata_select <- c("None", strata_list)
153	+	selectizeInput(session$ns("strata"), "Strata",
154	+	choices = strata_select, multiple = F,
155	+	selected = unlist(strata_select)[1]
156	+	)
157	+
158	+	})
159	+
160	+
161	+	observeEvent(input$subcheck, {
162	+	output$subvar <- renderUI({
163	+	req(input$subcheck == T)
164	+	req(!is.null(input$x_bar))
165	+
166	+	var_subgroup <- setdiff(names(data()), c(vlist()$except_vars, input$x_bar, input$y_bar, input$strata))
167	+
168	+	var_subgroup_list <- mklist(data_varStruct(), var_subgroup)
169	+	validate(
170	+	need(length(var_subgroup) > 0 , "No variables for sub-group analysis")
171	+	)
172	+
173	+	tagList(
174	+	selectInput(session$ns("subvar_km"), "Sub-group variables",
175	+	choices = var_subgroup_list, multiple = T,
176	+	selected = var_subgroup[1])
177	+	)
178	+
179	+
180	+	})
181	+
182	+	})
183	+
184	+
185	+	output$subval <- renderUI({
186	+	req(input$subcheck == T)
187	+	req(length(input$subvar_km) > 0)
188	+
189	+	outUI <- tagList()
190	+
191	+	for (v in seq_along(input$subvar_km)){
192	+	if (input$subvar_km[[v]] %in% vlist()$factor_vars){
193	+	outUI[[v]] <- selectInput(session$ns(paste0("subval_km", v)), paste0("Sub-group value: ", input$subvar_km[[v]]),
194	+	choices = data_label()[variable == input$subvar_km[[v]], level], multiple = T,
195	+	selected = data_label()[variable == input$subvar_km[[v]], level][1])
196	+	} else{
197	+	val <- stats::quantile(data()[[input$subvar_km[[v]]]], na.rm = T)
198	+	outUI[[v]] <- sliderInput(session$ns(paste0("subval_km", v)), paste0("Sub-group range: ", input$subvar_km[[v]]),
199	+	min = val[1], max = val[5],
200	+	value = c(val[2], val[4]))
201	+	}
202	+
203	+	}
204	+	outUI
205	+
206	+	})
207	+
208	+	barInput <- reactive({
209	+	req(c(input$x_bar, input$y_bar, input$strata))
210	+	data <- data.table(data())
211	+	label <- data_label()
212	+	color <- ifelse(input$strata == "None", "black", input$strata)
213	+	fill = "white"
214	+	if(input$fill){
215	+	fill <- ifelse(input$strata == "None", input$x_bar, input$strata)
216	+	}
217	+
218	+	if (input$strata != "None"){
219	+	data <- data[!is.na(get(input$strata))]
220	+	}
221	+	add.params <- list()
222	+	cor.coeff.args <- list(p.accuracy = 0.001)
223	+
224	+	add ="mean"
225	+	if (input$jitter){
226	+	add <- c("mean", "jitter")
227	+	}
228	+	if (input$mean){
229	+	add <- "mean_se"
230	+	}
231	+	if (input$mean & input$jitter){
232	+	add <- c("jitter", "mean_se")
233	+	}
234	+
235	+
236	+
237	+	ggpubr::ggbarplot(data, input$x_bar, input$y_bar, color = color, add = add, add.params = add.params, conf.int = input$lineci,
238	+	xlab = label[variable == input$x_bar, var_label][1],
239	+	ylab = label[variable == input$y_bar, var_label][1], na.rm = T,
240	+	position = position_dodge(),fill=fill,
241	+
242	+	)
243	+	})
244	+
245	+	output$downloadControls <- renderUI({
246	+	tagList(
247	+	column(4,
248	+	selectizeInput(session$ns("file_ext"), "File extension (dpi = 300)",
249	+	choices = c("jpg","pdf", "tiff", "svg", "pptx"), multiple = F,
250	+	selected = "pptx"
251	+	)
252	+	),
253	+	column(4,
254	+	sliderInput(session$ns("fig_width"), "Width (in):",
255	+	min = 5, max = 15, value = 8
256	+	)
257	+	),
258	+	column(4,
259	+	sliderInput(session$ns("fig_height"), "Height (in):",
260	+	min = 5, max = 15, value = 6
261	+	)
262	+	)
263	+	)
264	+	})
265	+
266	+	output$downloadButton <- downloadHandler(
267	+	filename = function() {
268	+	paste(input$x_bar, "_", input$y_bar,"_barplot.",input$file_ext ,sep="")
269	+
270	+	},
271	+	# content is a function with argument file. content writes the plot to the device
272	+	content = function(file) {
273	+	withProgress(message = 'Download in progress',
274	+	detail = 'This may take a while...', value = 0, {
275	+	for (i in 1:15) {
276	+	incProgress(1/15)
277	+	Sys.sleep(0.01)
278	+	}
279	+
280	+	if (input$file_ext == "pptx"){
281	+	my_vec_graph <- rvg::dml(ggobj = barInput())
282	+
283	+	doc <- officer::read_pptx()
284	+	doc <- officer::add_slide(doc, layout = "Title and Content", master = "Office Theme")
285	+	doc <- officer::ph_with(doc, my_vec_graph, location = officer::ph_location(width = input$fig_width, height = input$fig_height))
286	+	print(doc, target = file)
287	+
288	+	} else{
289	+	ggplot2::ggsave(file, barInput(), dpi = 300, units = "in", width = input$fig_width, height =input$fig_height)
290	+	}
291	+	})
292	+
293	+	}
294	+	)
295	+
296	+	return(barInput)
297	+
298	+
299	+
300	+
301	+
302	+	}
303	+	)
304	+
305	+
306	+
307	+
308	+
309	+
310	+
311	+
312	+
313	+
314	+
315	+
316	+
317	+
318	+
319	+
320	+
321	+
322	+	}
323	+	#####
324	+
325	+
326	+	#
327	+	#
328	+	# ui <- fluidPage(
329	+	# sidebarLayout(
330	+	# sidebarPanel(
331	+	# barUI("bar")
332	+	# ),
333	+	# mainPanel(
334	+	# plotOutput("bar_plot"),
335	+	# ggplotdownUI("bar")
336	+	# )
337	+	# )
338	+	# )
339	+	#
340	+	# server <- function(input, output, session) {
341	+	# mtcars$am <- as.factor(mtcars$am)
342	+	# mtcars$vs <- as.factor(mtcars$vs)
343	+	# mtcars$gear <- as.factor(mtcars$gear)
344	+	# mtcars$carb <- as.factor(mtcars$carb)
345	+	# mtcars$cyl <- as.factor(mtcars$cyl)
346	+	# data <- reactive(mtcars)
347	+	# data.label <- reactive(jstable::mk.lev(mtcars))
348	+	# out_bar <- barServer("bar", data = data, data_label = data.label,
349	+	# data_varStruct = NULL)
350	+	#
351	+	# output$bar_plot <- renderPlot({
352	+	# print(out_bar())
353	+	# })
354	+	# }
355	+	#
356	+	# shinyApp(ui, server)

Files		•	•	•	Coverage
R	6,905	411	0	6,494	5.95%
Project Totals (22 files)	6,905	411	0	6,494	5.95%

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423	456		tb <- out_tb1()$table
424	457		cap <- out_tb1()$caption
425	458		out.tb1 <- datatable(tb, rownames = T, extensions = "Buttons", caption = cap,
426		-	options = c(jstable::opt.tb1("tb1"),
427		-	list(columnDefs = list(list(visible=FALSE, targets= which(colnames(tb) %in% c("test","sig"))))
428		-	),
429		-	list(scrollX = TRUE)
430		-	)
	459	+	options = c(jstable::opt.tb1("tb1"),
	460	+	list(columnDefs = list(list(visible=FALSE, targets= which(colnames(tb) %in% c("test","sig"))))
	461	+	),
	462	+	list(scrollX = TRUE)
	463	+	)
431	464		)
432	465		if ("sig" %in% colnames(tb)){
433	466		out.tb1 = out.tb1 %>% formatStyle("sig", target = 'row' ,backgroundColor = styleEqual("**", 'yellow'))

490	523		print(out_scatter())
491	524		})
492	525
	526	+	out_box <- boxServer("box", data = data, data_label = data.label, data_varStruct = NULL, nfactor.limit = nfactor.limit)
	527	+
	528	+	output$box_plot <- renderPlot({
	529	+	print(out_box())
	530	+	})
	531	+
	532	+	out_bar <- barServer("bar", data = data, data_label = data.label, data_varStruct = NULL, nfactor.limit = nfactor.limit)
	533	+
	534	+	output$bar_plot <- renderPlot({
	535	+	print(out_bar())
	536	+	})
	537	+
	538	+	out_line <- lineServer("line", data = data, data_label = data.label, data_varStruct = NULL, nfactor.limit = nfactor.limit)
	539	+
	540	+	output$line_plot <- renderPlot({
	541	+	print(out_line())
	542	+	})
	543	+
493	544		out_kaplan <- callModule(kaplanModule, "kaplan", data = data, data_label = data.label, data_varStruct = NULL, nfactor.limit = nfactor.limit)
494	545
495	546		output$kaplan_plot <- renderPlot({

844	928		print(out_scatter())
845	929		})
846	930
	931	+	out_box <- boxServer("box", data = data, data_label = data.label, data_varStruct = NULL, nfactor.limit = nfactor.limit)
	932	+
	933	+	output$box_plot <- renderPlot({
	934	+	print(out_box())
	935	+	})
	936	+
	937	+	out_bar <- barServer("bar", data = data, data_label = data.label, data_varStruct = NULL, nfactor.limit = nfactor.limit)
	938	+
	939	+	output$bar_plot <- renderPlot({
	940	+	print(out_bar())
	941	+	})
	942	+
	943	+	out_line <- lineServer("line", data = data, data_label = data.label, data_varStruct = NULL, nfactor.limit = nfactor.limit)
	944	+
	945	+	output$line_plot <- renderPlot({
	946	+	print(out_line())
	947	+	})
	948	+
	949	+
847	950		out_kaplan <- callModule(kaplanModule, "kaplan", data = data, data_label = data.label, data_varStruct = NULL, nfactor.limit = nfactor.limit)
848	951
849	952		output$kaplan_plot <- renderPlot({

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