Last updated: 2022-07-27

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Here we create a small plot to show the tissue sample sizes.

Load the packages used in the analysis.

library(ggplot2)
library(cowplot)

These are the tissues that were included in the mr.mash analyses.

tissues <-
  c("Brain_Substantia_nigra",
    "Uterus",
    "Brain_Anterior_cingulate_cortex_BA24",
    "Small_Intestine_Terminal_Ileum",
    "Brain_Spinal_cord_cervical_c-1",
    "Brain_Putamen_basal_ganglia",
    "Brain_Hippocampus",
    "Brain_Frontal_Cortex_BA9",
    "Brain_Amygdala",
    "Brain_Hypothalamus",
    "Minor_Salivary_Gland",
    "Brain_Cerebellar_Hemisphere",
    "Brain_Caudate_basal_ganglia",
    "Brain_Nucleus_accumbens_basal_ganglia", 
    "Vagina",
    "Ovary",
    "Artery_Coronary",
    "Prostate",
    "Brain_Cortex",
    "Esophagus_Gastroesophageal_Junction",
    "Spleen",
    "Cells_EBV-transformed_lymphocytes",
    "Adrenal_Gland",
    "Brain_Cerebellum",
    "Colon_Sigmoid",
    "Breast_Mammary_Tissue",
    "Stomach",
    "Colon_Transverse",
    "Heart_Atrial_Appendage",
    "Artery_Aorta",
    "Pituitary",
    "Esophagus_Muscularis",
    "Adipose_Visceral_Omentum",
    "Heart_Left_Ventricle",
    "Skin_Not_Sun_Exposed_Suprapubic",
    "Pancreas",
    "Adipose_Subcutaneous",
    "Liver",
    "Nerve_Tibial",
    "Lung",
    "Esophagus_Mucosa",
    "Skin_Sun_Exposed_Lower_leg",
    "Cells_Cultured_fibroblasts",
    "Artery_Tibial",
    "Thyroid",
    "Muscle_Skeletal",
    "Testis",
    "Whole_Blood")

Read in the tissue sample sizes:

dat <- read.csv("data/gtex-v8-sample-size-by-tissue.csv",
                stringsAsFactors = FALSE)

These are the tissue sample sizes:

rownames(dat) <- dat$Tissue
dat <- dat[tissues,c("Tissue","RNASeq.and.Genotyped.samples")]
names(dat) <- c("tissue","sample_size")
print(dat,row.names = FALSE)
#                                 tissue sample_size
#                 Brain_Substantia_nigra         114
#                                 Uterus         129
#   Brain_Anterior_cingulate_cortex_BA24         147
#         Small_Intestine_Terminal_Ileum         174
#         Brain_Spinal_cord_cervical_c-1         126
#            Brain_Putamen_basal_ganglia         170
#                      Brain_Hippocampus         165
#               Brain_Frontal_Cortex_BA9         175
#                         Brain_Amygdala         129
#                     Brain_Hypothalamus         170
#                   Minor_Salivary_Gland         144
#            Brain_Cerebellar_Hemisphere         175
#            Brain_Caudate_basal_ganglia         194
#  Brain_Nucleus_accumbens_basal_ganglia         202
#                                 Vagina         141
#                                  Ovary         167
#                        Artery_Coronary         213
#                               Prostate         221
#                           Brain_Cortex         205
#    Esophagus_Gastroesophageal_Junction         330
#                                 Spleen         227
#      Cells_EBV-transformed_lymphocytes         147
#                          Adrenal_Gland         233
#                       Brain_Cerebellum         209
#                          Colon_Sigmoid         318
#                  Breast_Mammary_Tissue         396
#                                Stomach         324
#                       Colon_Transverse         368
#                 Heart_Atrial_Appendage         372
#                           Artery_Aorta         387
#                              Pituitary         237
#                   Esophagus_Muscularis         465
#               Adipose_Visceral_Omentum         469
#                   Heart_Left_Ventricle         386
#        Skin_Not_Sun_Exposed_Suprapubic         517
#                               Pancreas         305
#                   Adipose_Subcutaneous         581
#                                  Liver         208
#                           Nerve_Tibial         532
#                                   Lung         515
#                       Esophagus_Mucosa         497
#             Skin_Sun_Exposed_Lower_leg         605
#             Cells_Cultured_fibroblasts         483
#                          Artery_Tibial         584
#                                Thyroid         574
#                        Muscle_Skeletal         706
#                                 Testis         322
#                            Whole_Blood         670

Scale the area of the circles in the plot by the sample size of each tissue:

n <- nrow(dat)
p <- ggplot(dat,aes(x = 1:n,y = 1,size = sqrt(sample_size))) +
  geom_point(shape = 21,fill = "black",color = "white") +
  scale_x_continuous(breaks = 1:n) +
  scale_size_continuous(range = c(1,6),breaks = sqrt(c(125,200,400,700))) +
  theme_cowplot(font_size = 10)
print(p)

ggsave("sample_sizes.eps",p,height = 2,width = 7)

sessionInfo()
# R version 3.6.2 (2019-12-12)
# Platform: x86_64-apple-darwin15.6.0 (64-bit)
# Running under: macOS Catalina 10.15.7
# 
# Matrix products: default
# BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
# LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
# 
# locale:
# [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
# 
# attached base packages:
# [1] stats     graphics  grDevices utils     datasets  methods   base     
# 
# other attached packages:
# [1] cowplot_1.1.1 ggplot2_3.3.6
# 
# loaded via a namespace (and not attached):
#  [1] Rcpp_1.0.8        highr_0.8         pillar_1.6.2      compiler_3.6.2   
#  [5] bslib_0.3.1       later_1.0.0       jquerylib_0.1.4   git2r_0.29.0     
#  [9] workflowr_1.7.0   tools_3.6.2       digest_0.6.23     gtable_0.3.0     
# [13] jsonlite_1.7.2    evaluate_0.14     lifecycle_1.0.0   tibble_3.1.3     
# [17] pkgconfig_2.0.3   rlang_0.4.11      DBI_1.1.0         yaml_2.2.0       
# [21] xfun_0.29         fastmap_1.1.0     withr_2.5.0       dplyr_1.0.7      
# [25] stringr_1.4.0     knitr_1.37        systemfonts_1.0.2 generics_0.0.2   
# [29] fs_1.5.2          vctrs_0.3.8       sass_0.4.0        tidyselect_1.1.1 
# [33] rprojroot_1.3-2   grid_3.6.2        glue_1.4.2        R6_2.4.1         
# [37] fansi_0.4.0       rmarkdown_2.11    farver_2.0.1      purrr_0.3.4      
# [41] magrittr_2.0.1    whisker_0.4       scales_1.1.0      backports_1.1.5  
# [45] promises_1.1.0    ellipsis_0.3.2    htmltools_0.5.2   assertthat_0.2.1 
# [49] colorspace_1.4-1  httpuv_1.5.2      ragg_0.3.1        labeling_0.3     
# [53] utf8_1.1.4        stringi_1.4.3     munsell_0.5.0     crayon_1.4.1