I need to plot a gene of interest in only fibroblast cells, however, when I use ImageDimPlot, it keeps showing the expression of the gene in all tissue, although I subsetted the data to only fibroblast.

I know that I have x and y coordinates of the genes in each cell and also x and y coordinates of the cells, however, they are different and the only way I might be able to plot what I am looking for is with defining a threshold for the coordinates of the gene and the cells, however, it won't be visually accurate enough.

I have tried this:

# cell identities: set based on the "subset" metadata.
Idents(nano.obj_all) <- nano.obj_all$subset

# Create a new metadata column 'plot_group' with two levels:
# "Epithelial" for cells where subset equals "epi", and "Other" for all other cells.
nano.obj_all$plot_group <- ifelse(nano.obj_all$subset == "epi", "Epithelial", "Other")

# Define the cells to plot based on the desired identities.
cells_to_plot <- WhichCells(nano.obj_all, idents = c("epi", "stroma", "myeloids", "tcells", "plasmas"))

# Loop in each fov, create an ImageDimPlot and use the custom group,
# Ensure that cell identities are set based on the "subset" metadata.
Idents(nano.obj_all) <- nano.obj_all$subset

# Create a new metadata column 'plot_group' with two levels:
# "Epithelial" for cells where subset equals "epi", and "Other" for all other cells.
nano.obj_all$plot_group <- ifelse(nano.obj_all$subset == "epi", "Epithelial", "Other")

# Force the factor levels to match exactly
nano.obj_all$plot_group <- factor(nano.obj_all$plot_group, levels = c("Epithelial", "Other"))

# Define the cells to plot based on the desired identities.
cells_to_plot <- WhichCells(nano.obj_all, idents = c("epi", "stroma", "myeloids", "tcells", "plasmas"))

# Define the fields of view (fovs).
fovs <- c("Hia", "Hib", "Hic", "Cia", "Cib", "Cic", "Uia", "Uib", "Uic")

# Loop in each fov, create an ImageDimPlot using the custom group, and save the plot as a PNG file.
for (f in fovs) {
  p <- ImageDimPlot(nano.obj_all, 
                    fov = f,
                    cells = cells_to_plot,
                    molecules = "ABL1",
                    group.by = "plot_group",  # use the new group column for coloring
                    size = 0.6,
                    cols = c("Epithelial" = "#4A82F7", "Other" = "#F0B041"),  # assign colors manually
  ) + labs(title = f)
    ggsave(filename = paste0("ImageDimPlot_CellType_", f, ".png"),
         plot = p,
         width = 12,
         height = 12,
         dpi = 350)
  
  cat("Saved plot for fov:", f, "\n")
}