Nothing
## ---- echo = FALSE--------------------------------------------------------------------------------
options(width = 100)
## -------------------------------------------------------------------------------------------------
library(iCOBRA)
data(cobradata_example)
class(cobradata_example)
cobradata_example
## -------------------------------------------------------------------------------------------------
cobradata_example <- calculate_adjp(cobradata_example)
## -------------------------------------------------------------------------------------------------
cobraperf <- calculate_performance(cobradata_example, binary_truth = "status",
cont_truth = "logFC", splv = "none",
maxsplit = 4)
slotNames(cobraperf)
## -------------------------------------------------------------------------------------------------
cobraplot <- prepare_data_for_plot(cobraperf, colorscheme = "Dark2",
facetted = TRUE)
## ---- fig.width = 7, fig.height = 4, fig.cap = "", warning = FALSE--------------------------------
plot_tpr(cobraplot)
## ---- fig.width = 7, fig.height = 4, fig.cap = "", warning = FALSE--------------------------------
plot_fdrtprcurve(cobraplot)
## ---- fig.width = 7, fig.height = 4, fig.cap = "", warning = FALSE--------------------------------
plot_overlap(cobraplot)
## ---- fig.width = 7, fig.height = 5, warning = FALSE----------------------------------------------
cobraperf <- calculate_performance(cobradata_example, binary_truth = "status",
cont_truth = "status", splv = "expr_cat")
cobraplot <- prepare_data_for_plot(cobraperf, colorscheme = "Dark2",
facetted = TRUE)
plot_tpr(cobraplot)
## ---- fig.width = 7, fig.height = 5, warning = FALSE----------------------------------------------
library(ggplot2)
pp <- plot_tpr(cobraplot, stripsize = 7.5, pointsize = 3)
pp + theme(axis.text.x = element_text(angle = 90, vjust = 0.5,
hjust = 1, size = 10),
axis.text.y = element_text(size = 10),
axis.title.x = element_text(size = 10),
axis.title.y = element_text(size = 10))
## ---- fig.width = 7, fig.height = 4, warning = FALSE----------------------------------------------
pp + theme(axis.text.x = element_text(angle = 90, vjust = 0.5,
hjust = 1, size = 10),
axis.text.y = element_text(size = 10),
axis.title.x = element_text(size = 10),
axis.title.y = element_text(size = 10),
legend.position = "bottom") +
facet_wrap(~splitval, nrow = 1)
## ---- fig.width = 7, fig.height = 5, warning = FALSE----------------------------------------------
plot_overlap(cobraplot)
plot_overlap(cobraplot, cex = c(1, 0.7, 0.7))
## ---- fig.width = 7, fig.height = 5, warning = FALSE----------------------------------------------
cobraplot <- prepare_data_for_plot(cobraperf,
colorscheme = c("blue", "green", "pink"),
facetted = TRUE)
pp <- plot_tpr(cobraplot, stripsize = 7.5, pointsize = 3)
pp + theme(axis.text.x = element_text(angle = 90, vjust = 0.5,
hjust = 1, size = 10),
axis.text.y = element_text(size = 10),
axis.title.x = element_text(size = 10),
axis.title.y = element_text(size = 10))
## ---- eval = FALSE--------------------------------------------------------------------------------
# COBRAapp(cobradata_example)
# COBRAapp()
## -------------------------------------------------------------------------------------------------
COBRAData_to_text(cobradata = cobradata_example,
truth_file = "cobradata_truth.txt",
result_files = "cobradata_results.txt",
feature_id = "feature")
## -------------------------------------------------------------------------------------------------
cobra <- COBRAData_from_text(truth_file = "cobradata_truth.txt",
result_files = "cobradata_results.txt",
feature_id = "feature")
cobra
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