画细胞比例图，如何指定分组顺序？

[terry676L]

scRNAtoolVis这个包画比例图，如何指定分组顺序吗？factor指定好像没起作用

[terry676L]

cellRatioPlot(object = scobj,
sample.name = "group",
celltype.name = "celltype",
fill.col = use_colors,
flow.curve = 0.5,
levels = c())

cellRatioPlot <- function(
object = NULL,
sample.name = NULL,
celltype.name = NULL,
col.width = 0.7,
flow.alpha = 0.25,
flow.curve = 0,
fill.col = NULL,
levels = NULL) {

获取元数据

meta <- [email protected]

如果指定了levels，则设置因子水平

if (!is.null(levels)) {
meta[[sample.name]] <- factor(meta[[sample.name]], levels = levels)
}

计算百分比比率

ratio.info <- meta %>%
dplyr::group_by(.data[[sample.name]], .data[[celltype.name]]) %>%
dplyr::summarise(num = n()) %>%
dplyr::mutate(rel_num = num / sum(num))

设置颜色

if (is.null(fill.col)) {
fill.col <- jjAnno::useMyCol("paired", n = length(unique(meta[, celltype.name])))
}

绘图

p <-
ggplot2::ggplot(
ratio.info,
ggplot2::aes_string(x = sample.name, y = "rel_num")
) +
ggplot2::geom_col(
ggplot2::aes_string(fill = celltype.name),
width = col.width
) +
ggalluvial::geom_flow(
ggplot2::aes_string(
stratum = celltype.name,
alluvium = celltype.name,
fill = celltype.name
),
width = 0.5,
alpha = flow.alpha,
knot.pos = flow.curve
) +
ggplot2::theme_bw() +
ggplot2::coord_cartesian(expand = 0) +
ggplot2::scale_y_continuous(labels = scales::label_percent()) +
ggplot2::scale_fill_manual(
values = fill.col,
name = "Cell Type"
) +
ggplot2::theme(
panel.grid = ggplot2::element_blank(),
axis.text = ggplot2::element_text(size = ggplot2::rel(1.2), color = "black"),
axis.title = ggplot2::element_text(size = ggplot2::rel(1.5), color = "black"),
legend.text = ggplot2::element_text(size = ggplot2::rel(1.2), color = "black"),
legend.title = ggplot2::element_text(size = ggplot2::rel(1.5), color = "black")
) +
ggplot2::xlab("") +
ggplot2::ylab("Cell percent ratio")

return(p)
}

[terry676L]

修改函数，增加levels，已解决！

[junjunlab]

你可以重新安装一下，使用 sample.order 指定样本顺序。