supporting the main plot with coord_fixed

[xiangpin]

• This pr update the method of accessors
• updating the internal function to support the main plot with coord_fixed
  • this feature can be used to visualize the result of spatial omics.

{library(aplot)
library(SpatialExperiment)
library(SingleCellExperiment)
library(SVP)
library(ggsc)
library(ggplot2)
library(STexampleData)
library(scater)
} |> suppressPackageStartupMessages()


spe <- STexampleData::Visium_humanDLPFC()

spe <- spe[,!is.na(spe$ground_truth)]

spe <- spe[rowSums(counts(spe)>0)>0,]
spe <- spe |> logNormCounts()

#spe <- runDetectSVG(spe)
#svDf(spe) |> dplyr::arrange(rank) |> head()

p1 <- spe |> sc_spatial(
         features='ENSG00000197971',
         mapping = aes(x= pxl_row_in_fullres, y = pxl_col_in_fullres),
         geom=geom_bgpoint,pointsize=1.5, image.plot=F, slot=2
         ) +
       ggtitle(NULL)

da <- p1$data |>
    dplyr::select(pxl_col_in_fullres, pxl_row_in_fullres, ground_truth)

theme_subplot <- list(xlab(NULL),
                      ylab(NULL),
                      theme_bw(),
                      theme(panel.grid=element_blank()
                      )
)

p.t <- da |>
    dplyr::mutate(row=round(pxl_row_in_fullres)) |>
    dplyr::group_by(row, ground_truth) |>
    dplyr::summarize(row_prop=100*dplyr::n()/nrow(da)) |>
    ggplot(aes(x=row,y=ground_truth,fill=ground_truth, alpha=row_prop)) +
    geom_tile() +
    theme_subplot +
    guides(x = 'none') +
    scale_fill_brewer(palette = 'Set2')


p.r <- da |>
    dplyr::mutate(col=round(pxl_col_in_fullres)) |>
    dplyr::group_by(col, ground_truth) |>
    dplyr::summarize(col_prop=100*dplyr::n()/nrow(da)) |>
    ggplot(aes(y=col,x=ground_truth,fill=ground_truth, alpha=col_prop)) +
    geom_tile() +
    theme_subplot +
    guides(y='none',x=guide_axis(angle=-45)) +
    scale_fill_brewer(palette='Set2')


pp <- p1 |> insert_top(p.t, height=.2) |> insert_right(p.r, width=.23)