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feature added: layer_symbol() supports "freetext", and add color, size options #107

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feature added: layer_symbol() supports "freetext", and add color, size options #107

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25abe46
layer_symol supports freetext or character column, and color, size op…
Jan 10, 2023
44de015
export layer_symbol function
Jan 10, 2023
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2 changes: 2 additions & 0 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@ export(annotation_point)
export(annotation_tile)
export(as_ComplexHeatmap)
export(heatmap)
export(layer_symbol)
export(layer_arrow_down)
export(layer_arrow_up)
export(layer_diamond)
Expand Down Expand Up @@ -40,6 +41,7 @@ importFrom(grDevices,colorRampPalette)
importFrom(grid,gpar)
importFrom(grid,grid.grabExpr)
importFrom(grid,grid.points)
importFrom(grid,grid.text)
importFrom(grid,unit)
importFrom(grid,unit.c)
importFrom(lifecycle,deprecate_warn)
Expand Down
29 changes: 24 additions & 5 deletions R/functions.R
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Expand Up @@ -446,7 +446,10 @@ add_annotation = function(my_input_heatmap,
#'
setGeneric("layer_symbol", function(.data,
...,
symbol = "point")
symbol = "point",
freetext = "",
color = "#161616",
size = 3)
standardGeneric("layer_symbol"))

#' layer_symbol
Expand All @@ -461,7 +464,10 @@ setGeneric("layer_symbol", function(.data,
#'
setMethod("layer_symbol", "InputHeatmap", function(.data,
...,
symbol = "point"){
symbol = "point",
freetext = "",
color = "#161616",
size = 3){

.data_drame = .data@data

Expand All @@ -474,7 +480,8 @@ setMethod("layer_symbol", "InputHeatmap", function(.data,
arrow_up = 24,
arrow_down = 25,
star = 8,
asterisk = 42
asterisk = 42,
freetext = 0
)

if(!symbol %in% names(symbol_dictionary) | length(symbol) != 1)
Expand Down Expand Up @@ -502,8 +509,20 @@ setMethod("layer_symbol", "InputHeatmap", function(.data,
row = !!.vertical %>% as.factor() %>% as.integer()
) |>
filter(...) |>
select(column, row) |>
mutate(shape = symbol_dictionary[[symbol]])
mutate(
shape = symbol_dictionary[[symbol]],
freetext = !!enquo(freetext),
color = !!enquo(color),
size = !!enquo(size)
) %>%
# {
# if(!is.null(freetext_col)){
# mutate(freetext = !!enquo(freetext_col)) %>%
# }else{
# mutate(freetext = "") %>%
# }
# } %>%
select(column, row, shape, freetext, color, size)
)

.data
Expand Down
26 changes: 17 additions & 9 deletions R/methods.R
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Expand Up @@ -36,7 +36,7 @@ InputHeatmap<-setClass(
left_annotation = tibble(col_name = character(), orientation = character(), col_orientation = character(), data = list(), fx = list(), annot = list(), annot_type= character(), idx = integer(), color = list(), further_arguments = list()),
group_top_annotation = list(),
group_left_annotation = list(),
layer_symbol = tibble(column = integer(), row = integer(), shape = integer())
layer_symbol = tibble(column = integer(), row = integer(), shape = integer(), freetext = character(), color = character(), size = integer())
)
)

Expand All @@ -49,8 +49,8 @@ InputHeatmap<-setClass(
#'
#' @importFrom methods show
#' @importFrom tibble rowid_to_column
#' @importFrom grid grid.points
#'
#' @importFrom grid grid.points grid.text
#'
#'
#' @name as_ComplexHeatmap
#'
Expand Down Expand Up @@ -130,15 +130,23 @@ setMethod("as_ComplexHeatmap", "InputHeatmap", function(tidyHeatmap){

# Filter just points to label
inner_join(tidyHeatmap@layer_symbol, by = c("row", "column")) |>
select(`index_column_wise`, `shape`)
select(`index_column_wise`, `shape`, `freetext`, `color`, `size`)

if(nrow(ind)>0)
ind_symbol = ind %>% filter(shape != 0)
ind_freetext = ind %>% filter(shape == 0)
if(nrow(ind_symbol)>0)
grid.points(
x[ind$index_column_wise], y[ind$index_column_wise],
pch = ind$shape ,
size = unit(3, "mm"),
gp = gpar(col = NULL, fill="#161616")
x[ind_symbol$index_column_wise], y[ind_symbol$index_column_wise],
pch = ind_symbol$shape ,
size = unit(ind_symbol$size, "mm"),
gp = gpar(col = NULL, fill=ind_symbol$color)
)

if(nrow(ind_freetext) > 0){
grid.text(
ind_freetext$freetext, x[ind_freetext$index_column_wise], y[ind_freetext$index_column_wise],
gp = gpar(fontsize = ind_freetext$size, col = ind_freetext$color))
}
}

return(do.call(Heatmap, tidyHeatmap@input))
Expand Down