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Fix transpose in normalization step #19

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Merged
Bisaloo merged 6 commits into from
May 6, 2026
+9 −5
Merged

Fix transpose in normalization step #19

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952ab79
Fix transpose in normalization step
Bisaloo May 4, 2026
60ea42a
Apply special channel selection and normalization to rgb images
Bisaloo May 4, 2026
3c0dea9
Ensure rgb settings get applied to pal
Bisaloo May 4, 2026
df18584
Use %||% shorthand to define pal
Bisaloo May 4, 2026
3175d95
Do not plot legend in RGB imgs
Bisaloo May 4, 2026
08451f2
Fix channel selection in rgb images
Bisaloo May 5, 2026
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14 changes: 9 additions & 5 deletions R/plotImage.R
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Original file line number Diff line number Diff line change
Expand Up @@ -101,8 +101,8 @@ NULL
cl <- matrix(cl, ncol=2)
}
colors_rgb <- col2rgb(c)
normed_a <- (t(linear_a) - cl[, 1]) / (cl[, 2] - cl[, 1])
flat_img <- tcrossprod(colors_rgb, normed_a) / d
normed_a <- (linear_a - cl[, 1]) / (cl[, 2] - cl[, 1])
flat_img <- (colors_rgb %*% normed_a) / d
flat_img |>
t() |>
farver::encode_colour() |>
Expand Down Expand Up @@ -142,7 +142,6 @@ NULL
#' @importFrom SpatialData channels
#' @noRd
.ch_idx <- \(x, ch) {
if (.is_rgb(x)) return(seq_len(3))
if (is.null(ch)) return(1)
lbs <- channels(x)
if (all(ch %in% lbs)) {
Expand Down Expand Up @@ -205,9 +204,14 @@ setMethod("plotImage", "SpatialData", \(x, i=1, j=1, k=NULL, ch=NULL, c=NULL, cl
j <- CTname(y)[j]
y <- transform(y, j)
wh <- .get_wh(y)
if (.is_rgb(y)) {
# RGB: we plot everything by default and we don't normalize
ch <- ch %||% channels(y)
cl <- cl %||% c(0, 1/3)
}
df <- .df_i(y, k, ch, c, cl)
pal <- if (is.null(c)) .DEFAULT_COLORS else c
if (dim(y)[1] > 1) {
pal <- c %||% .DEFAULT_COLORS
if (dim(y)[1] > 1 && !.is_rgb(y)) {
nms <- unlist(channels(y))[idx <- .ch_idx(y, ch)]
pal <- pal[seq_along(idx)]; names(pal) <- nms
}
Expand Down
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