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Improved URL presets
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-Passing parameters through URL has been improved
-Color presets implemented
-Plot size presets corrected
-criterion preset implemented
-rotate plot preset implemented
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@JoachimGoedhart
JoachimGoedhart committed Apr 20, 2020
1 parent 057b8e0 commit fedfb57
Showing 1 changed file with 33 additions and 35 deletions.
68 changes: 33 additions & 35 deletions app.R
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Original file line number Diff line number Diff line change
Expand Up @@ -69,7 +69,7 @@ ui <- fluidPage(
h4("Selection & Annotation of hits"),
sliderInput("fc_cutoff", "Fold Change threshold:", -5, 5, step=0.1, value = c(-1.5,1.5)),
sliderInput("p_cutoff", "Significance threshold:", 0, 5, step=0.1, value = 2),
selectInput("direction", label="Use thresholds to annotate:", choices = list("All (ignores thresholds)"="all", "Changed (and significant)"="significant","Increased (and significant)"="increased", "Decreased (and significant)"="decreased"), selected ="all"),
selectInput("direction", label="Use thresholds to annotate:", choices = list("All (ignores thresholds)"="all", "Changed (and significant)"="significant","Increased (and significant)"="increased", "Decreased (and significant)"="decreased"), selected ="significant"),

selectInput("criterion", label="Criterion for ranking hits:", choices = list("Manhattan distance"="manh", "Euclidean distance"="euclid","Fold change"="fc","Significance"="sig"), selected ="manh"),

Expand Down Expand Up @@ -554,7 +554,7 @@ observe({
updateSliderInput(session, "fc_cutoff", value = unlist(strsplit(presets_vis[3],",")))
updateSliderInput(session, "p_cutoff", value = presets_vis[4])
updateSelectInput(session, "direction", selected = presets_vis[5])
# updateSelectInput(session, "criterion", selected = presets_vis[6])
updateSelectInput(session, "criterion", selected = presets_vis[6])

}

Expand All @@ -573,21 +573,11 @@ observe({
# updateCheckboxInput(session, "user_selected", value= presets_can[4])
# updateTextInput(session, "user_gene_list", value= presets_can[4])


genelist.selected <<- unlist(strsplit(presets_can[4],","))

############
# updateSelectizeInput(session, "user_gene_list", choices = koos$Name)
# updateTextInput(session, "user_gene_list2", value= user_list)
#
# genelist.selected <<-user_list

#############

}




############ ?layout ################

if (!is.null(query[['layout']])) {
Expand All @@ -596,32 +586,33 @@ observe({
presets_layout <- unlist(strsplit(presets_layout,";"))
# observe(print((presets_layout)))

updateCheckboxInput(session, "rotate_plot", value = presets_layout[1])
# updateCheckboxInput(session, "no_grid", value = (presets_layout[2]))

updateCheckboxInput(session, "change_scale", value = presets_layout[3])
updateTextInput(session, "range_x", value= presets_layout[4])
updateTextInput(session, "range_y", value= presets_layout[5])
updateCheckboxInput(session, "transform", value = presets_layout[6])
# updateCheckboxInput(session, "transform", value = presets_layout[6])
# updateRadioButtons(session, "transform_x", selected = presets_layout[7])
# updateRadioButtons(session, "transform_y", selected = presets_layout[8])
# updateCheckboxInput(session, "add_description", value = presets_layout[9])
if (length(presets_layout)>10) {
updateNumericInput(session, "plot_height", value= presets_layout[10])
updateNumericInput(session, "plot_width", value= presets_layout[11])
if ((presets_layout[6])=='X') {
updateNumericInput(session, "plot_height", value= presets_layout[7])
updateNumericInput(session, "plot_width", value= presets_layout[8])
}
# updateTabsetPanel(session, "tabs", selected = "Plot")
}

############ ?color ################

# if (!is.null(query[['color']])) {
#
# presets_color <- query[['color']]
# presets_color <- unlist(strsplit(presets_color,";"))
#
# updateSelectInput(session, "colour_list", selected = presets_color[1])
# updateTextInput(session, "user_color_list", value= presets_color[2])
# }
if (!is.null(query[['color']])) {

presets_color <- query[['color']]
presets_color <- unlist(strsplit(presets_color,";"))

updateSelectInput(session, "adjustcolors", selected = presets_color[1])
updateTextInput(session, "user_color_list", value= presets_color[2])
}

############ ?label ################

Expand All @@ -645,9 +636,8 @@ observe({
updateNumericInput(session, "fnt_sz_cand", value= presets_label[10])
updateCheckboxInput(session, "add_legend", value = presets_label[11])
# updateTextInput(session, "legend_title", value= presets_label[12])
# updateCheckboxInput(session, "hide_labels_y", value = presets_label[13])

# updateCheckboxInput(session, "add_description", value = presets_label[9])


}


Expand Down Expand Up @@ -684,7 +674,7 @@ url <- reactive({
fc <- input$fc_cutoff
fc <- paste(fc, collapse=",")

vis <- c(input$pointSize, input$alphaInput, fc, input$p_cutoff, input$direction)
vis <- c(input$pointSize, input$alphaInput, fc, input$p_cutoff, input$direction, input$criterion)

#Convert the list of genes to a comma-seperated string
a <- input$user_gene_list
Expand All @@ -693,8 +683,16 @@ url <- reactive({
#as.character is necessary; if omitted TRUE is converted to 0 and FALSE to 1 which is undesired
can <- c(input$top_x, as.character(input$show_table), input$hide_labels, a)

layout <- c("", "", input$change_scale, input$range_x, input$range_y, "X", input$plot_height, input$plot_width)
layout <- c(input$rotate_plot, "", input$change_scale, input$range_x, input$range_y, "X", input$plot_height, input$plot_width)

#Hide the standard list of colors if it is'nt used
if (input$adjustcolors != "5") {
color <- c(input$adjustcolors, "none")
} else if (input$adjustcolors == "5") {
color <- c(input$adjustcolors, input$user_color_list)
}

############ COLOR ##########

label <- c(input$add_title, input$title, input$label_axes, input$lab_x, input$lab_y, input$adj_fnt_sz, input$fnt_sz_title, input$fnt_sz_labs, input$fnt_sz_ax, input$fnt_sz_cand, input$add_legend, input$legend_title, input$hide_labels_y)

Expand All @@ -717,9 +715,9 @@ url <- reactive({
layout <- paste(layout, collapse=";")
layout <- paste0("layout=", layout)
#
# color <- sub("FALSE", "", color)
# color <- paste(color, collapse=";")
# color <- paste0("color=", color)
color <- sub("FALSE", "", color)
color <- paste(color, collapse=";")
color <- paste0("color=", color)

label <- sub("FALSE", "", label)
label <- paste(label, collapse=";")
Expand All @@ -733,12 +731,12 @@ url <- reactive({

# parameters <- paste(data, vis,layout,color,label,stim,url, sep="&")

parameters <- paste(data,vis,can,layout,label,url, sep="&")
parameters <- paste(data,vis,can,layout,color,label,url, sep="&")


preset_URL <- paste(base_URL, parameters, sep="?")

# observe(print(parameters))
observe(print(parameters))
# observe(print(preset_URL))
return(preset_URL)
})
Expand Down

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