Which error bar to use to show gene expression from single-cell RNAseq data
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11 months ago
gundalav ▴ 370

I would like to show the single cell gene expression. My question is which one is preferable, using mean standard error (Fig 1) or box plot (Fig 2) in my plot?

enter image description here

Any explanation (or paper) that suggest why one method is prefers to other?

This is the R code I use to generate those figs:

library(tidyverse)
library(ggpubr)

dat <- structure(list(gexp = c(
  4.2, 11.5, 7.3, 5.8, 6.4, 10, 11.2, 11.2,
  5.2, 7, 16.5, 16.5, 15.2, 17.3, 22.5, 17.3, 13.6, 14.5, 18.8,
  15.5, 23.6, 18.5, 33.9, 25.5, 26.4, 32.5, 26.7, 21.5, 23.3, 29.5,
  15.2, 21.5, 17.6, 9.7, 14.5, 10, 8.2, 9.4, 16.5, 9.7, 19.7, 23.3,
  23.6, 26.4, 20, 25.2, 25.8, 21.2, 14.5, 27.3, 25.5, 26.4, 22.4,
  24.5, 24.8, 30.9, 26.4, 27.3, 29.4, 23
), supp = structure(c(
  2L,
  2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
  2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L,
  1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
  1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L
), .Label = c(
  "OJ",
  "VC"
), class = "factor"), dose = c(
  0.5, 0.5, 0.5, 0.5, 0.5, 0.5,
  0.5, 0.5, 0.5, 0.5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2,
  2, 2, 2, 2, 2, 2, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5,
  0.5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2,
  2
)), row.names = c(NA, -60L), class = c("tbl_df", "tbl", "data.frame"))


p1 <- ggbarplot(dat, x = "dose", y = "gexp", 
          add = "mean_se")

p2 <- ggboxplot(dat, x = "dose", y = "gexp")

cowplot::plot_grid(p1, p2, labels =  c("Fig 1", "Fig 2"))
expression rnaseq statistics gene single-cell • 395 views
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