Astrocyte case study

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Last updated: 2024-01-01

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Knit directory: mage_2020_marker-gene-benchmarking/

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library(SingleCellExperiment)

Loading required package: SummarizedExperiment

Loading required package: MatrixGenerics

Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges

Loading required package: stats4

Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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    expand.grid, I, unname

Loading required package: IRanges

Loading required package: GenomeInfoDb

Loading required package: Biobase

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

library(dplyr)

Attaching package: 'dplyr'

The following object is masked from 'package:Biobase':

    combine

The following objects are masked from 'package:GenomicRanges':

    intersect, setdiff, union

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    intersect

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    collapse, desc, intersect, setdiff, slice, union

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    first, intersect, rename, setdiff, setequal, union

The following objects are masked from 'package:BiocGenerics':

    combine, intersect, setdiff, union

The following object is masked from 'package:matrixStats':

    count

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

library(purrr)

Attaching package: 'purrr'

The following object is masked from 'package:GenomicRanges':

    reduce

The following object is masked from 'package:IRanges':

    reduce

library(tibble)
library(scater)

Loading required package: scuttle

Loading required package: ggplot2

astrocyte <- readRDS(here::here("data", "real_data", "astrocyte.rds"))

scanpy_default <- readRDS(
  here::here("results", "real_data", "astrocyte-scanpy_t_rankby_raw.rds")
)

seurat_default <- readRDS(
  here::here("results", "real_data", "astrocyte-seurat_wilcox.rds")
)

Work on Astro_THAL_Lat for now.

scanpy_default |> 
  pluck("result") |> 
  as_tibble() |> 
  filter(cluster == "Astro_THAL_lat")

# A tibble: 2,000 × 7
   cluster     gene  scaled_statistic   p_value p_value_adj log_fc raw_statistic
   <chr>       <chr>            <dbl>     <dbl>       <dbl>  <dbl>         <dbl>
 1 Astro_THAL… Trpm3             39.3 2.72e-206   5.44e-203   2.49             0
 2 Astro_THAL… Erbb4             31.9 1.96e-129   1.31e-126   2.72             0
 3 Astro_THAL… Kcnd2             31.5 3.79e-134   3.79e-131   2.53             0
 4 Astro_THAL… Aldh…             24.5 2.83e- 80   7.07e- 78   3.18             0
 5 Astro_THAL… Plcb1             22.2 1.39e- 75   2.54e- 73   1.92             0
 6 Astro_THAL… Slc4…             19.0 1.40e- 62   1.65e- 60   1.21             0
 7 Astro_THAL… Rgs6              18.5 7.71e- 58   7.01e- 56   1.73             0
 8 Astro_THAL… Lrp1b             16.8 1.12e- 50   8.65e- 49   1.30             0
 9 Astro_THAL… Nrxn3             16.6 3.83e- 47   2.64e- 45   2.22             0
10 Astro_THAL… Esrrg             15.9 1.66e- 43   1.04e- 41   2.72             0
# … with 1,990 more rows

seurat_default |> 
  pluck("result") |> 
  as_tibble() |> 
  filter(cluster == "Astro_THAL_lat")

# A tibble: 397 × 7
     p_value p_value_adj cluster     log_fc gene  raw_statistic scaled_statistic
       <dbl>       <dbl> <fct>        <dbl> <chr>         <dbl>            <dbl>
 1 4.54e-119   9.08e-116 Astro_THAL…   2.09 Aldh…             0                0
 2 5.66e-103   1.13e- 99 Astro_THAL…   1.47 Trpm3             0                0
 3 1.01e- 91   2.02e- 88 Astro_THAL…   1.35 Erbb4             0                0
 4 3.05e- 87   6.10e- 84 Astro_THAL…   1.37 Esrrg             0                0
 5 7.49e- 77   1.50e- 73 Astro_THAL…   1.27 Kcnd2             0                0
 6 6.60e- 75   1.32e- 71 Astro_THAL…  -1.61 Slc1…             0                0
 7 6.84e- 72   1.37e- 68 Astro_THAL…   1.18 Car10             0                0
 8 7.67e- 72   1.53e- 68 Astro_THAL…   1.39 Plcb1             0                0
 9 6.22e- 66   1.24e- 62 Astro_THAL…   1.36 Nrxn3             0                0
10 2.77e- 65   5.54e- 62 Astro_THAL…   1.10 Sntg1             0                0
# … with 387 more rows

Only Seurat finds Car10

scanpy_default |> 
  pluck("result") |> 
  as_tibble() |> 
  filter(cluster == "Astro_THAL_lat") |> 
  mutate(n = 1:n()) |> 
  filter(gene == "Car10")

# A tibble: 1 × 8
  cluster gene  scaled_statistic  p_value p_value_adj log_fc raw_statistic     n
  <chr>   <chr>            <dbl>    <dbl>       <dbl>  <dbl>         <dbl> <int>
1 Astro_… Car10             12.9 1.52e-31    5.16e-30   2.61             0    20

Astro_STR

Efemp1, Gfra1, Thbs4, Zfhx3

scanpy_default |> 
  pluck("result") |> 
  as_tibble() |> 
  filter(cluster == "Astro_STR")

# A tibble: 2,000 × 7
   cluster   gene   scaled_statistic  p_value p_value_adj log_fc raw_statistic
   <chr>     <chr>             <dbl>    <dbl>       <dbl>  <dbl>         <dbl>
 1 Astro_STR Slc1a2            12.4  1.37e-21    9.79e-20  1.21              0
 2 Astro_STR Prex2             11.5  2.30e-19    1.48e-17  1.48              0
 3 Astro_STR Cst3              10.5  3.49e-17    1.99e-15  1.60              0
 4 Astro_STR Malat1             9.21 1.50e-14    7.29e-13  0.495             0
 5 Astro_STR Zbtb20             8.05 3.53e-12    1.50e-10  0.764             0
 6 Astro_STR Mgat5              7.37 1.11e-10    3.84e- 9  1.72              0
 7 Astro_STR Tspan7             7.06 3.77e-10    1.23e- 8  1.21              0
 8 Astro_STR Rmst               6.85 1.15e- 9    3.66e- 8  1.59              0
 9 Astro_STR Gfra1              6.18 2.42e- 8    6.72e- 7  2.26              0
10 Astro_STR Gnao1              6.17 2.13e- 8    6.09e- 7  1.04              0
# … with 1,990 more rows

seurat_default |> 
  pluck("result") |> 
  as_tibble() |> 
  filter(cluster == "Astro_STR")

# A tibble: 234 × 7
    p_value p_value_adj cluster   log_fc gene   raw_statistic scaled_statistic
      <dbl>       <dbl> <fct>      <dbl> <chr>          <dbl>            <dbl>
 1 6.16e-21    1.23e-17 Astro_STR -3.05  Kcnd2              0                0
 2 4.70e-19    9.40e-16 Astro_STR  0.920 Gfra1              0                0
 3 9.43e-18    1.89e-14 Astro_STR  1.28  Cst3               0                0
 4 2.42e-16    4.83e-13 Astro_STR  1.01  Prex2              0                0
 5 2.57e-16    5.14e-13 Astro_STR -1.41  Lrp1b              0                0
 6 5.43e-16    1.09e-12 Astro_STR  1.02  Rcan2              0                0
 7 4.72e-15    9.44e-12 Astro_STR  0.798 Slc1a2             0                0
 8 9.44e-14    1.89e-10 Astro_STR  1.19  Mgat5              0                0
 9 2.06e-13    4.11e-10 Astro_STR  0.430 Malat1             0                0
10 3.42e-13    6.84e-10 Astro_STR -2.30  Erbb4              0                0
# … with 224 more rows

plotExpression(astrocyte, x = "label", "Prex2")

plotExpression(astrocyte, x = "label", "Cst3")

plotExpression(astrocyte, x = "label", "Mgat5")

Kcnd2 down-regulated

scanpy_default |> 
  pluck("result") |> 
  as_tibble() |> 
  filter(cluster == "Astro_HPC")

# A tibble: 2,000 × 7
   cluster   gene   scaled_statistic  p_value p_value_adj log_fc raw_statistic
   <chr>     <chr>             <dbl>    <dbl>       <dbl>  <dbl>         <dbl>
 1 Astro_HPC Slc1a2            18.2  1.93e-55    5.50e-53  1.08              0
 2 Astro_HPC Tspan7            12.4  1.34e-29    1.58e-27  1.17              0
 3 Astro_HPC Wdr17             12.2  6.60e-29    6.95e-27  0.882             0
 4 Astro_HPC Ptprt             11.4  1.63e-25    1.30e-23  1.12              0
 5 Astro_HPC Tcf4              11.1  1.96e-24    1.35e-22  1.09              0
 6 Astro_HPC Slc1a3            10.1  1.60e-21    9.14e-20  0.800             0
 7 Astro_HPC Lsamp             10.1  5.19e-21    2.88e-19  0.602             0
 8 Astro_HPC Gnao1             10.0  6.05e-21    3.27e-19  1.01              0
 9 Astro_HPC Cadps              9.86 8.80e-20    3.91e-18  2.84              0
10 Astro_HPC Clmn               9.82 6.06e-20    3.03e-18  1.30              0
# … with 1,990 more rows

seurat_default |> 
  pluck("result") |> 
  as_tibble() |> 
  filter(cluster == "Astro_HPC")

# A tibble: 305 × 7
    p_value p_value_adj cluster   log_fc gene   raw_statistic scaled_statistic
      <dbl>       <dbl> <fct>      <dbl> <chr>          <dbl>            <dbl>
 1 3.47e-59    6.94e-56 Astro_HPC  1.09  Cadps              0                0
 2 4.61e-53    9.22e-50 Astro_HPC -2.73  Kcnd2              0                0
 3 3.37e-43    6.74e-40 Astro_HPC -2.54  Erbb4              0                0
 4 1.61e-42    3.22e-39 Astro_HPC -1.96  Trpm3              0                0
 5 2.38e-42    4.75e-39 Astro_HPC -1.57  Fry                0                0
 6 1.40e-34    2.80e-31 Astro_HPC -1.48  Gabbr2             0                0
 7 2.20e-32    4.40e-29 Astro_HPC  0.674 Slc1a2             0                0
 8 5.23e-30    1.05e-26 Astro_HPC -2.22  Gria1              0                0
 9 1.05e-28    2.10e-25 Astro_HPC -0.961 Fgf14              0                0
10 8.24e-28    1.65e-24 Astro_HPC  0.859 Tcf4               0                0
# … with 295 more rows

plotExpression(astrocyte, x = "label", "Slc1a2")

plotExpression(astrocyte, x = "label", "Pdgfd")

plotExpression(astrocyte, x = "label", "Cadps")

plotExpression(astrocyte, x = "label", "Kcnd2")

Session information

devtools::session_info()

─ Session info  ──────────────────────────────────────────────────────────────
 hash: flag: Bolivia, woman singer: dark skin tone, headphone

 setting  value
 version  R version 4.1.2 (2021-11-01)
 os       Red Hat Enterprise Linux 9.2 (Plow)
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  en_AU.UTF-8
 ctype    en_AU.UTF-8
 tz       Australia/Melbourne
 date     2024-01-01
 pandoc   2.18 @ /apps/easybuild-2022/easybuild/software/MPI/GCC/11.3.0/OpenMPI/4.1.4/RStudio-Server/2022.07.2+576-Java-11-R-4.1.2/bin/pandoc/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
 package              * version  date (UTC) lib source
 assertthat             0.2.1    2019-03-21 [2] CRAN (R 4.1.2)
 beachmat               2.10.0   2021-10-26 [1] Bioconductor
 beeswarm               0.4.0    2021-06-01 [2] CRAN (R 4.1.2)
 Biobase              * 2.54.0   2021-10-26 [1] Bioconductor
 BiocGenerics         * 0.40.0   2021-10-26 [1] Bioconductor
 BiocNeighbors          1.12.0   2021-10-26 [1] Bioconductor
 BiocParallel           1.28.3   2021-12-09 [1] Bioconductor
 BiocSingular           1.10.0   2021-10-26 [1] Bioconductor
 bitops                 1.0-7    2021-04-24 [2] CRAN (R 4.1.2)
 bslib                  0.3.1    2021-10-06 [1] CRAN (R 4.1.0)
 cachem                 1.0.6    2021-08-19 [1] CRAN (R 4.1.0)
 callr                  3.7.0    2021-04-20 [2] CRAN (R 4.1.2)
 cli                    3.6.1    2023-03-23 [1] CRAN (R 4.1.0)
 colorspace             2.1-0    2023-01-23 [1] CRAN (R 4.1.0)
 cowplot                1.1.1    2020-12-30 [2] CRAN (R 4.1.2)
 crayon                 1.5.1    2022-03-26 [1] CRAN (R 4.1.0)
 DBI                    1.1.2    2021-12-20 [1] CRAN (R 4.1.0)
 DelayedArray           0.20.0   2021-10-26 [1] Bioconductor
 DelayedMatrixStats     1.16.0   2021-10-26 [1] Bioconductor
 desc                   1.4.0    2021-09-28 [2] CRAN (R 4.1.2)
 devtools               2.4.2    2021-06-07 [2] CRAN (R 4.1.2)
 digest                 0.6.29   2021-12-01 [1] CRAN (R 4.1.0)
 dplyr                * 1.0.9    2022-04-28 [1] CRAN (R 4.1.0)
 ellipsis               0.3.2    2021-04-29 [2] CRAN (R 4.1.2)
 evaluate               0.14     2019-05-28 [2] CRAN (R 4.1.2)
 fansi                  1.0.4    2023-01-22 [1] CRAN (R 4.1.0)
 farver                 2.1.1    2022-07-06 [1] CRAN (R 4.1.0)
 fastmap                1.1.0    2021-01-25 [2] CRAN (R 4.1.2)
 fs                     1.5.2    2021-12-08 [1] CRAN (R 4.1.0)
 generics               0.1.3    2022-07-05 [1] CRAN (R 4.1.0)
 GenomeInfoDb         * 1.30.0   2021-10-26 [1] Bioconductor
 GenomeInfoDbData       1.2.7    2021-12-03 [1] Bioconductor
 GenomicRanges        * 1.46.1   2021-11-18 [1] Bioconductor
 ggbeeswarm             0.6.0    2017-08-07 [2] CRAN (R 4.1.2)
 ggplot2              * 3.3.6    2022-05-03 [1] CRAN (R 4.1.0)
 ggrepel                0.9.1    2021-01-15 [2] CRAN (R 4.1.2)
 git2r                  0.28.0   2021-01-10 [2] CRAN (R 4.1.2)
 glue                   1.6.0    2021-12-17 [1] CRAN (R 4.1.0)
 gridExtra              2.3      2017-09-09 [2] CRAN (R 4.1.2)
 gtable                 0.3.0    2019-03-25 [2] CRAN (R 4.1.2)
 here                   1.0.1    2020-12-13 [1] CRAN (R 4.1.0)
 highr                  0.9      2021-04-16 [2] CRAN (R 4.1.2)
 htmltools              0.5.2    2021-08-25 [1] CRAN (R 4.1.0)
 httpuv                 1.6.5    2022-01-05 [1] CRAN (R 4.1.0)
 IRanges              * 2.28.0   2021-10-26 [1] Bioconductor
 irlba                  2.3.5    2021-12-06 [1] CRAN (R 4.1.0)
 jquerylib              0.1.4    2021-04-26 [2] CRAN (R 4.1.2)
 jsonlite               1.8.0    2022-02-22 [1] CRAN (R 4.1.0)
 knitr                  1.36     2021-09-29 [1] CRAN (R 4.1.0)
 labeling               0.4.2    2020-10-20 [2] CRAN (R 4.1.2)
 later                  1.3.0    2021-08-18 [1] CRAN (R 4.1.0)
 lattice                0.20-45  2021-09-22 [2] CRAN (R 4.1.2)
 lifecycle              1.0.1    2021-09-24 [1] CRAN (R 4.1.0)
 magrittr               2.0.3    2022-03-30 [1] CRAN (R 4.1.0)
 Matrix                 1.3-4    2021-06-01 [2] CRAN (R 4.1.2)
 MatrixGenerics       * 1.6.0    2021-10-26 [1] Bioconductor
 matrixStats          * 0.62.0   2022-04-19 [1] CRAN (R 4.1.0)
 memoise                2.0.1    2021-11-26 [1] CRAN (R 4.1.0)
 munsell                0.5.0    2018-06-12 [2] CRAN (R 4.1.2)
 pillar                 1.7.0    2022-02-01 [1] CRAN (R 4.1.0)
 pkgbuild               1.2.0    2020-12-15 [2] CRAN (R 4.1.2)
 pkgconfig              2.0.3    2019-09-22 [2] CRAN (R 4.1.2)
 pkgload                1.2.3    2021-10-13 [2] CRAN (R 4.1.2)
 prettyunits            1.1.1    2020-01-24 [2] CRAN (R 4.1.2)
 processx               3.5.2    2021-04-30 [2] CRAN (R 4.1.2)
 promises               1.2.0.1  2021-02-11 [2] CRAN (R 4.1.2)
 ps                     1.7.1    2022-06-18 [1] CRAN (R 4.1.0)
 purrr                * 0.3.4    2020-04-17 [2] CRAN (R 4.1.2)
 R6                     2.5.1    2021-08-19 [1] CRAN (R 4.1.0)
 Rcpp                   1.0.8.3  2022-03-17 [1] CRAN (R 4.1.0)
 RCurl                  1.98-1.5 2021-09-17 [1] CRAN (R 4.1.0)
 remotes                2.4.2    2021-11-30 [1] CRAN (R 4.1.0)
 rlang                  1.0.3    2022-06-27 [1] CRAN (R 4.1.0)
 rmarkdown              2.14     2022-04-25 [1] CRAN (R 4.1.0)
 rprojroot              2.0.3    2022-04-02 [1] CRAN (R 4.1.0)
 rstudioapi             0.14     2022-08-22 [1] CRAN (R 4.1.0)
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 [1] /home/jpullin/R/x86_64-pc-linux-gnu-library/4.1
 [2] /apps/easybuild-2022/easybuild/software/MPI/GCC/11.3.0/OpenMPI/4.1.4/R/4.1.2/lib64/R/library

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