Macosko: P14 mouse retina

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Last updated: 2022-10-26

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Knit directory: Williams_Retina_scRNA_IMPG2_workflowr/

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Data acquisition

Single-cell RNA-seq data from the P14 mouse retina corresponding to Macosko et al 2015 were retrieved from GEO accession GSE63472. A csv file mapping cell barcodes to clusters was additionally downloaded from the McCarroll lab website. Below we additionally annotate the cluster numbers into named cell types based on the information in Fig. 5D

Analysis of IMPG1 and IMPG2 expression in retinal cell types

Load libraries

suppressPackageStartupMessages(library(tidyverse))
suppressPackageStartupMessages(library(cowplot))

Import metadata

meta <- read_tsv("GSE63472_retina_clusteridentities.txt", col_names = c("CellID", "Cluster")) %>%
    mutate(Category = case_when(
        Cluster == 1 ~ "Horizontal cells",
        Cluster == 2 ~ "Retinal ganglion cells",
        Cluster %in% 3:23 ~ "Amacrine cells",
        Cluster == 24 ~ "Rods",
        Cluster == 25 ~ "Cones",
        Cluster %in% 26:33 ~ "Bipolar cells",
        Cluster == 34 ~ "Muller glia",
        Cluster == 35 ~ "Astrocytes",
        Cluster == 36 ~ "Fibroblasts",
        Cluster == 37 ~ "Vascular endothelium",
        Cluster == 38 ~ "Pericytes",
        Cluster == 39 ~ "Microglia"
        )
    )

Filter expression matrix for IMPG1 and IMPG2 expression

grep -E 'gene|IMPG1|IMPG2' GSE63472_P14Retina_merged_digital_expression.txt > GSE63472_P14Retina_merged_digital_expression_IMPG1-IMPG2.tsv

Import expression data

Only retain cells in named clusters

mouse.tbl <- read_tsv("GSE63472_P14Retina_merged_digital_expression_IMPG1-IMPG2.tsv", name_repair = "minimal") %>%
    pivot_longer(cols=!gene,names_to="CellID",values_to="Expression") %>%
    inner_join(meta,by="CellID") %>%
    pivot_wider(names_from=gene,values_from=Expression)

Plot boxplots of IMPG1 and IMPG2 expression

p1 <- mouse.tbl %>%
    group_by(Category) %>%
    ggplot(aes(x=reorder(Category,-IMPG2),y=log10(IMPG1+0.1))) +
    geom_boxplot(outlier.shape = NA) +
    theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5),legend.position = c(0.7, 0.8)) +
    xlab("Mouse retina cell types") +
    ylab("log10 IMPG1 expression")

p2 <- mouse.tbl %>%
    group_by(Category) %>%
    ggplot(aes(x=reorder(Category,-IMPG2),y=log10(IMPG2+0.1))) +
    geom_boxplot(outlier.shape = NA) +
    theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5),legend.position = c(0.7, 0.8)) +
    xlab("Mouse retina cell types") +
    ylab("log10 IMPG2 expression")

plot_grid(p1,p2)

Past versions of unnamed-chunk-7-1.png

Version	Author	Date
146a845	jeremymsimon	2022-10-26

Session information

sessionInfo()

R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.5 (Ootpa)

Matrix products: default
BLAS/LAPACK: /nas/longleaf/rhel8/apps/r/4.1.0/lib/libopenblas_haswellp-r0.3.5.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] cowplot_1.1.1   forcats_0.5.1   stringr_1.4.0   dplyr_1.0.9    
 [5] purrr_0.3.4     readr_2.1.2     tidyr_1.2.0     tibble_3.1.8   
 [9] ggplot2_3.3.6   tidyverse_1.3.1 workflowr_1.7.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8.3     lubridate_1.8.0  getPass_0.2-2    ps_1.6.0        
 [5] assertthat_0.2.1 rprojroot_2.0.2  digest_0.6.29    utf8_1.2.2      
 [9] R6_2.5.1         cellranger_1.1.0 backports_1.4.1  reprex_2.0.1    
[13] evaluate_0.15    highr_0.9        httr_1.4.2       pillar_1.7.0    
[17] rlang_1.0.4      readxl_1.3.1     rstudioapi_0.13  whisker_0.4     
[21] callr_3.7.0      jquerylib_0.1.4  rmarkdown_2.12   labeling_0.4.2  
[25] bit_4.0.4        munsell_0.5.0    broom_1.0.0      compiler_4.1.0  
[29] httpuv_1.6.5     modelr_0.1.8     xfun_0.30        pkgconfig_2.0.3 
[33] htmltools_0.5.2  tidyselect_1.1.2 fansi_1.0.3      withr_2.5.0     
[37] crayon_1.5.1     tzdb_0.2.0       dbplyr_2.1.1     later_1.3.0     
[41] grid_4.1.0       jsonlite_1.8.0   gtable_0.3.0     lifecycle_1.0.1 
[45] DBI_1.1.2        git2r_0.30.1     magrittr_2.0.2   scales_1.2.0    
[49] vroom_1.5.7      cli_3.3.0        stringi_1.7.6    farver_2.1.0    
[53] fs_1.5.2         promises_1.2.0.1 xml2_1.3.3       bslib_0.3.1     
[57] ellipsis_0.3.2   generics_0.1.2   vctrs_0.4.1      tools_4.1.0     
[61] bit64_4.0.5      glue_1.6.2       hms_1.1.1        parallel_4.1.0  
[65] processx_3.5.2   fastmap_1.1.0    yaml_2.3.5       colorspace_2.0-3
[69] rvest_1.0.2      knitr_1.37       haven_2.4.3      sass_0.4.0