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Play with RowTreePlot visual params
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@RiboRings
RiboRings committed Jun 19, 2024
1 parent 5dd0c70 commit 972a280
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4 changes: 2 additions & 2 deletions DESCRIPTION
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Expand Up @@ -40,8 +40,8 @@ Suggests:
testthat (>= 3.0.0),
utils,
vegan
URL: https://github.com/RiboRings/iSEEtree
BugReports: https://github.com/RiboRings/iSEEtree/issues
URL: https://github.com/microbiome/iSEEtree
BugReports: https://github.com/microbiome/iSEEtree/issues
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
VignetteBuilder: knitr
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1 change: 1 addition & 0 deletions NAMESPACE
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Expand Up @@ -58,6 +58,7 @@ importFrom(miaViz,plotRowTree)
importFrom(shiny,plotOutput)
importFrom(shiny,renderPlot)
importFrom(shinyWidgets,addSpinner)
importFrom(utils,stack)
importMethodsFrom(iSEE,.generateOutput)
importMethodsFrom(iSEE,.panelColor)
importMethodsFrom(iSEE,.renderOutput)
1 change: 1 addition & 0 deletions R/class-AbundancePlot.R
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Expand Up @@ -283,6 +283,7 @@ setMethod(".definePanelTour", "AbundancePlot", function(x) {

#' @importFrom SummarizedExperiment rowData
#' @importFrom mia taxonomyRanks
#' @importFrom utils stack
.list_taxa <- function(se){

row_data <- as.data.frame(rowData(se)[ , taxonomyRanks(se)])
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73 changes: 38 additions & 35 deletions R/class-RowTreePlot.R
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Expand Up @@ -138,15 +138,14 @@ setMethod(".createObservers", "RowTreePlot",
panel_name <- .getEncodedName(x)

.createProtectedParameterObservers(panel_name, c("layout", "add_legend",
"RowSelectionSource", "order_tree", "visual_parameters", "size_parameters",
"RowSelectionSource", "order_tree", "size_parameters", "visual_parameters",
"shape_parameters", "colour_parameters"), input=input, pObjects=pObjects,
rObjects=rObjects)

.createUnprotectedParameterObservers(panel_name, c("edge_colour_by",
"tip_colour_by", "tip_size_by", "tip_shape_by", "node_size_by",
"node_shape_by", "node_clour_by", "edge_size_by", "node_size_by",
"node_colour_by", "node_shape_by"), input=input, pObjects=pObjects,
rObjects=rObjects)
"node_shape_by", "node_colour_by", "edge_size_by"), input=input,
pObjects=pObjects, rObjects=rObjects)

invisible(NULL)
})
Expand Down Expand Up @@ -189,30 +188,22 @@ setMethod(".generateOutput", "RowTreePlot",
args[["add_legend"]] <- deparse(slot(x, "add_legend"))
args[["order_tree"]] <- deparse(slot(x, "order_tree"))

ifelse (slot(x, "colour_parameters") == "Edge",
args[["edge_colour_by"]] <- deparse(slot(x, "edge_colour_by")), 1)

ifelse ( slot(x, "colour_parameters") == "Node",
args[["node_colour_by"]] <- deparse(slot(x, "node_colour_by")), 1)

ifelse ( slot(x, "colour_parameters") == "Tip",
args[["tip_colour_by"]] <- deparse(slot(x, "tip_colour_by")), 1)

ifelse ( slot(x, "size_parameters") == "Edge",
args[["edge_size_by"]] <- deparse(slot(x, "edge_size_by")), 1)

ifelse ( slot(x, "size_parameters") == "Node",
args[["node_size_by"]] <- deparse(slot(x, "node_size_by")), 1)

ifelse ( slot(x, "size_parameters") == "Tip",
args[["tip_size_by"]] <- deparse(slot(x, "tip_size_by")), 1)
if( "Colour" %in% slot(x, "visual_parameters") ){
args <- .assign_viz_param(args, x, "Edge", "colour")
args <- .assign_viz_param(args, x, "Node", "colour")
args <- .assign_viz_param(args, x, "Tip", "colour")
}

ifelse ( slot(x, "shape_parameters") == "Node",
args[["node_shape_by"]] <- deparse(slot(x, "node_shape_by")), 1)
if( "Shape" %in% slot(x, "visual_parameters") ){
args <- .assign_viz_param(args, x, "Node", "shape")
args <- .assign_viz_param(args, x, "Tip", "shape")
}

ifelse ( slot(x, "shape_parameters") == "Tip",
args[["tip_shape_by"]] <- deparse(slot(x, "tip_shape_by")), 1)

if( "Size" %in% slot(x, "visual_parameters") ){
args <- .assign_viz_param(args, x, "Edge", "size")
args <- .assign_viz_param(args, x, "Node", "size")
args <- .assign_viz_param(args, x, "Tip", "size")
}

args <- sprintf("%s=%s", names(args), args)
args <- paste(args, collapse=", ")
Expand Down Expand Up @@ -376,16 +367,16 @@ setMethod(".definePanelTour", "RowTreePlot", function(x) {
collapseBox(paste0(panel_name, "_VisualBoxOpen"),
title="Visual parameters", open=FALSE,
# Tree layout
.checkboxGroupInput.iSEE(x, field="visual_parameters", label="Visual parameters:",
.checkboxGroupInput.iSEE(x, field="visual_parameters", label=NULL,
inline=TRUE, selected=slot(x, "visual_parameters"),
choices=c("Colour", "Size", "Shape")),

.conditionalOnCheckGroup(
paste0(panel_name, "_visual_parameters"), "Colour",
list(
.checkboxGroupInput.iSEE(x, field="colour_parameters", label="Colour by:",
.checkboxGroupInput.iSEE(x, field="colour_parameters",
inline=TRUE, selected=slot(x, "colour_parameters"),
choices=c("Edge", "Node", "Tip")),
choices=c("Edge", "Node", "Tip"), label="Colour by:"),
.conditionalOnCheckGroup(
paste0(panel_name, "_colour_parameters"), "Edge",
.selectInput.iSEE(x, field="edge_colour_by",
Expand All @@ -405,9 +396,9 @@ setMethod(".definePanelTour", "RowTreePlot", function(x) {
.conditionalOnCheckGroup(
paste0(panel_name, "_visual_parameters"), "Size",
list(
.checkboxGroupInput.iSEE(x, field="size_parameters", label="Size by:",
.checkboxGroupInput.iSEE(x, field="size_parameters",
inline=TRUE, selected=slot(x, "size_parameters"),
choices=c("Edge", "Node", "Tip")),
choices=c("Edge", "Node", "Tip"), label="Size by:"),
.conditionalOnCheckGroup(
paste0(panel_name, "_size_parameters"), "Edge",
.selectInput.iSEE(x, field="edge_size_by",
Expand All @@ -421,15 +412,15 @@ setMethod(".definePanelTour", "RowTreePlot", function(x) {
.conditionalOnCheckGroup(
paste0(panel_name, "_size_parameters"), "Tip",
.selectInput.iSEE(x, field="tip_size_by",
label="Size tips by", choices=names(rowData(se)),
selected=slot(x, "tip_size_by"))))),
label="Size tips by", choices=names(rowData(se)),
selected=slot(x, "tip_size_by"))))),

.conditionalOnCheckGroup(
paste0(panel_name, "_visual_parameters"), "Shape",
list(
.checkboxGroupInput.iSEE(x, field="shape_parameters", label="Shape by:",
.checkboxGroupInput.iSEE(x, field="shape_parameters",
inline=TRUE, selected=slot(x, "shape_parameters"),
choices=c("Node", "Tip")),
choices=c("Node", "Tip"), label="Shape by:"),
.conditionalOnCheckGroup(
paste0(panel_name, "_shape_parameters"), "Node",
.selectInput.iSEE(x, field="node_shape_by",
Expand All @@ -450,3 +441,15 @@ setMethod(".definePanelTour", "RowTreePlot", function(x) {
.checkboxInput.iSEE(x, field="add_legend", label="View legend",
value=slot(x, "add_legend")))
}

#' @importFrom methods slot
.assign_viz_param <- function(args, x, element, aesthetic) {

param_name <- paste(tolower(element), aesthetic, "by", sep = "_")

if( element %in% slot(x, paste(aesthetic, "parameters", sep = "_")) ){
args[[param_name]] <- deparse(slot(x, param_name))
}

return(args)
}

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