## ----install_cape, eval = FALSE-----------------------------------------------
# install.packages("cape")
## ----load_cape, echo = FALSE, warning = FALSE, error = FALSE, message = FALSE----
set.seed(1234)
library(cape)
## ----here, eval = FALSE-------------------------------------------------------
# install.packages("here")
# library("here")
## ----load_here, echo = FALSE--------------------------------------------------
library("here")
## ----read_csv_format----------------------------------------------------------
data_file <- here("demo", "demo_qtl", "data", "NON_NZO_Reifsnyder_pgm_CAPE_num.csv")
param_file <- here("demo", "demo_qtl", "0_NON_NZO.parameters_0.yml")
cross <- read_population(data_file)
cross_obj <- cape2mpp(cross)
obesity_cross <- cross_obj$data_obj
obesity_geno <- cross_obj$geno_obj$geno
## ----read_qtl2, eval = FALSE--------------------------------------------------
# iron_qtl2 <- read_cross2("https://kbroman.org/qtl2/assets/sampledata/iron/iron.yaml")
#
# iron_cape <- qtl2_to_cape(cross = iron_qtl2)
# data_obj <- iron_cape$data_obj
# geno_obj <- iron_cape$geno_obj
## ----read_plink, eval = FALSE-------------------------------------------------
# data_path <- here("demo", "demo_PLINK", "data")
# ped <- file.path(data_path, "test.ped")
# map <- file.path(data_path, "test.map")
# pheno <- file.path(data_path, "test.pheno")
# out <- file.path(data_path, "test.csv")
# param_file <- here("demo", "demo_PLINK", "0_plink.parameters_0.yml")
#
# cross_obj <- plink2cape(ped, map, pheno, out = "out.csv")
#
# data_obj <- cross_obj$data_obj
# geno_obj <- cross_obj$geno_obj$geno
## ----pheno_hist, fig.width = 7, fig.height = 3--------------------------------
hist_pheno(obesity_cross, pheno_which = c("BW_24", "INS_24", "log_GLU_24"))
## ----qnorm_pheno, fig.width = 7, fig.height = 3-------------------------------
qnorm_pheno(obesity_cross, pheno_which = c("BW_24", "INS_24", "log_GLU_24"))
## ----norm_pheno---------------------------------------------------------------
obesity_cross <- norm_pheno(obesity_cross, mean_center = TRUE)
## ----norm_qq, fig.width = 7, fig.height = 3-----------------------------------
qnorm_pheno(obesity_cross, pheno_which = c("BW_24", "INS_24", "log_GLU_24"))
## ----pheno_cor, fig.width = 5, fig.height = 5---------------------------------
plot_pheno_cor(obesity_cross, pheno_which = c("BW_24", "INS_24", "log_GLU_24"),
color_by = "pgm", group_labels = c("Non-obese", "Obese"))
## ----run_cape-----------------------------------------------------------------
param_file <- here("demo", "demo_qtl", "0_NON_NZO.parameters_0.yml")
results_path <- here("demo", "demo_qtl")
final_cross <- run_cape(obesity_cross, obesity_geno, results_file = "NON_NZO",
p_or_q = 0.05, verbose = FALSE, param_file = param_file, results_path = results_path)
## ----eigentraits, fig.width = 4, fig.height = 4-------------------------------
plot_svd(final_cross)
## ----single_plot, eval = FALSE------------------------------------------------
# singlescan_obj <- readRDS(here("demo", "demo_qtl", "results", "NON_NZO_singlescan.RDS"))
# plot_singlescan(final_cross, singlescan_obj, line_type = "h", lwd = 2,
# covar_label_size = 1)
## ----single_plot_fig1, results = "asis", echo = FALSE-------------------------
et1_fig <- here::here("vignettes", "Singlescan_ET1_Standardized.jpg")
cat(paste0("![](", et1_fig, "){width=70%}\n"))
## ----single_plot_fig2, results = "asis", echo = FALSE-------------------------
et2_fig <- here::here("vignettes", "Singlescan_ET2_Standardized.jpg")
cat(paste0("![](", et2_fig, "){width=70%}\n"))
## ----reparam_fig, results = "asis", echo = FALSE------------------------------
reparam_file <- here::here("vignettes", "reparam.png")
cat(paste0("![](", reparam_file, "){width=50%}\n"))
## ----var_inf, fig.height = 6, fig.width = 7-----------------------------------
plot_variant_influences(final_cross, show_alleles = FALSE)
## ----circ_net, fig.height = 6, fig.width = 6----------------------------------
plot_network(final_cross)
## ----net_vis, echo = FALSE, fig.width = 6, fig.height = 6---------------------
plot_full_network(final_cross, zoom = 1.2, node_radius = 0.3,
label_nodes = TRUE, label_offset = 0.4, label_cex = 0.5, bg_col = "lightgray",
arrow_length = 0.1, layout_matrix = "layout_with_kk", legend_position = "topright",
edge_lwd = 1, legend_radius = 2, legend_cex = 0.7, xshift = -1)
## ----plot_effects_line, fig.width = 7, fig.height = 3-------------------------
plot_effects(data_obj = final_cross, geno_obj = obesity_geno,
marker1 = "D15Mit72_B", marker1_label = "Chr15", plot_type = "l",
error_bars = "se")
## ----plot_int, fig.width = 7, fig.height = 3----------------------------------
plot_effects(data_obj = final_cross, geno_obj = obesity_geno,
marker1 = "D2Mit120_B", marker2 = "D15Mit72_B", marker1_label = "Chr2",
marker2_label = "Chr15", plot_type = "l", error_bars = "se")
## ----int_bar, fig.width = 7, fig.height = 3-----------------------------------
plot_effects(data_obj = final_cross, geno_obj = obesity_geno,
marker1 = "D2Mit120_B", marker2 = "D15Mit72_B", marker1_label = "Chr2",
marker2_label = "Chr15", plot_type = "b", error_bars = "se")
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