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Merge pull request #59 from jiajic/gg_image
fix: rework image plotting
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| Package: GiottoVisuals | ||
| Title: Visuals for the Giotto spatial biology analysis ecosystem | ||
| Version: 0.1.3 | ||
| Version: 0.1.4 | ||
| Authors@R: c( | ||
| person("Ruben", "Dries", email = "[email protected]", | ||
| role = c("aut", "cre")), | ||
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@@ -82,6 +82,8 @@ Collate: | |
| 'colorRamp2.R' | ||
| 'color_palettes.R' | ||
| 'dd.R' | ||
| 'generics.R' | ||
| 'gg_annotation_raster.R' | ||
| 'gg_info_layers.R' | ||
| 'globals.R' | ||
| 'gstop.R' | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,4 @@ | ||
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| # internals | ||
| setOldClass("gg") | ||
| setGeneric("gg_annotation_raster", function(ggobj, gimage, ...) standardGeneric("gg_annotation_raster")) |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,113 @@ | ||
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| #' @name gg_annotation_raster | ||
| #' @keywords internal | ||
| #' @title Append image to ggplot as annotation_raster | ||
| #' @param ggobj ggplot2 `gg` object | ||
| #' @param gimage `giottoLargeImage`, `giottoImage` or `list` thereof | ||
| #' @return `gg` object with images to plot appended as annotation rasters | ||
| NULL | ||
|
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| #' @rdname gg_annotation_raster | ||
| setMethod( | ||
| "gg_annotation_raster", | ||
| signature(ggobj = "gg", gimage = "list"), | ||
| function(ggobj, gimage, ...) | ||
| { | ||
| for(i in seq_along(gimage)) { | ||
| ggobj <- gg_annotation_raster(ggobj, gimage[[i]], ...) | ||
| } | ||
| return(ggobj) | ||
| } | ||
| ) | ||
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| #' @rdname gg_annotation_raster | ||
| setMethod( | ||
| "gg_annotation_raster", | ||
| signature(ggobj = "gg", gimage = "giottoImage"), | ||
| function(ggobj, gimage, ...) | ||
| { | ||
| # extract min and max from object | ||
| my_xmax = gimage@minmax[1] | ||
| my_xmin = gimage@minmax[2] | ||
| my_ymax = gimage@minmax[3] | ||
| my_ymin = gimage@minmax[4] | ||
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| # convert giotto image object into array | ||
| img_array = as.numeric(gimage@mg_object[[1]]) | ||
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| # extract adjustments from object | ||
| xmax_b = gimage@boundaries[1] | ||
| xmin_b = gimage@boundaries[2] | ||
| ymax_b = gimage@boundaries[3] | ||
| ymin_b = gimage@boundaries[4] | ||
|
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| # append to ggobj | ||
| ggobj <- ggobj + annotation_raster( | ||
| img_array, | ||
| xmin = my_xmin-xmin_b, xmax = my_xmax+xmax_b, | ||
| ymin = my_ymin-ymin_b, ymax = my_ymax+ymax_b | ||
| ) | ||
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| # TODO geom_raster to accommodate single-channel | ||
| return(ggobj) | ||
| } | ||
| ) | ||
|
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| #' @rdname gg_annotation_raster | ||
| setMethod( | ||
| "gg_annotation_raster", | ||
| signature(ggobj = "gg", gimage = "giottoLargeImage"), | ||
| function(ggobj, gimage, ...) | ||
| { | ||
| # get plotting minmax | ||
| extent = terra::ext(gimage@raster_object)[1:4] | ||
| xmin = extent[['xmin']] | ||
| xmax = extent[['xmax']] | ||
| ymin = extent[['ymin']] | ||
| ymax = extent[['ymax']] | ||
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| # convert raster object into array with 3 channels | ||
| img_array = terra::as.array(gimage@raster_object) | ||
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| # TODO: check if required, fixes NaN values | ||
| # replacing NA's by zero or another value directly in raster object? | ||
| # raster[is.na(raster[])] <- 0 | ||
| if (is.nan(max(img_array[,,1]))) { | ||
| img_array[,,1][is.nan(img_array[,,1])] = max(img_array[,,1], na.rm = TRUE) | ||
| } | ||
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| if(dim(img_array)[3] > 1) { | ||
| if(is.nan(max(img_array[,,2]))) { | ||
| img_array[,,2][is.nan(img_array[,,2])] = max(img_array[,,2], na.rm = TRUE) | ||
| } | ||
| } | ||
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| if(dim(img_array)[3] > 2) { | ||
| if(is.nan(max(img_array[,,3]))) { | ||
| img_array[,,3][is.nan(img_array[,,3])] = max(img_array[,,3], na.rm = TRUE) | ||
| } | ||
| } | ||
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| img_array = img_array/max(img_array, na.rm = TRUE) | ||
| if(dim(img_array)[3] == 1) { | ||
| img_array_RGB = array(NA, dim = c(dim(img_array)[1:2],3)) | ||
| img_array_RGB[,,1:3] = img_array | ||
| } else { | ||
| img_array_RGB = img_array | ||
| } | ||
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| # handle NA values | ||
| img_array_RGB[is.na(img_array_RGB)] <- 0 | ||
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| # append to ggobj | ||
| ggobj <- ggobj + annotation_raster( | ||
| img_array_RGB, | ||
| xmin = xmin, xmax = xmax, | ||
| ymin = ymin, ymax = ymax | ||
| ) | ||
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| # TODO geom_raster to accommodate single-channel | ||
| return(ggobj) | ||
| } | ||
| ) | ||
|
|
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