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Collection of R notebooks to enable local iAtlas plotting and functionality.

R 0.03% Jupyter Notebook 99.97%

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iatlas-notebooks's Issues

Update Readme

Update readme to include recent notebooks, e.g. API example module, ICI hazard ratio
Where appropriate , match language (e.g. title ) to that corresponding module in the app

Possible iatlas.api.client library loading error in ici_models_logistic_regression.ipynb

iatlas.api.client included in CRAN library loading but not found there .
Error message

Loading required package: iatlas.api.client

Warning message in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
“there is no package called ‘iatlas.api.client’”
Warning message:
“package ‘iatlas.api.client’ is not available for this version of R

Replacing current block

# We have a few libraries to install.
try({
    packages = c("magrittr", "wrapr", "dplyr", "tidyr", "plotly", "caret", "glmnet", "survminer", 
                 "dplyr", "arrow", "tidyr", "ggplot2", "pROC", "pheatmap", "knitr", "ggfortify", "iatlas.api.client")

    sapply(packages, function(x) {
      if (!require(x,character.only = TRUE))
        install.packages(x)
        suppressPackageStartupMessages(library(x,character.only = TRUE))
    })

    # and our iatlas package from github
    if (!require(iatlas.modules)) {
      devtools::install_github("CRI-iAtlas/iatlas.modules")
      suppressPackageStartupMessages(library(iatlas.modules))
    }},
    silent=TRUE 
)

with

# We have a few libraries to install.
try({
    # CRAN packages
    packages = c("magrittr", "wrapr", "dplyr", "tidyr", "plotly", "caret", "glmnet", "survminer", 
                 "dplyr", "arrow", "tidyr", "ggplot2", "pROC", "pheatmap", "knitr", "ggfortify")

    sapply(packages, function(x) {
      if (!require(x,character.only = TRUE))
        install.packages(x)
        suppressPackageStartupMessages(library(x,character.only = TRUE))
    })

    # and our iatlas.modules package from github
    if (!require(iatlas.modules)) {
      devtools::install_github("CRI-iAtlas/iatlas.modules")
      suppressPackageStartupMessages(library(iatlas.modules))
    }

    # and our iatlas.api.client package from github
    if (!require(iatlas.api.client)) {
      devtools::install_github("CRI-iAtlas/iatlas.api.client")
      suppressPackageStartupMessages(library(iatlas.modules))
    }},
    silent=TRUE 
)

The same seems to be true of other ici_models_*.ipynb

Check notebook_barplot function arguments

In cell_content_barplots.Rmd, section Cell content plots, there is a call to notebook_barplot with show_error_bars = NA (currenly line 128) gives error

Error in if (show_error_bars == TRUE) { : 
  missing value where TRUE/FALSE needed

README needs updating

Update to mention notebooks added since last iteration
Fix broken link to iAtlas logo

cell_content_barplots.Rmd may be looking to use jupyter notebook function embed_notebook

Executing

notebook_barplot(
  df,
  sort_by_var_choice = "Group", 
  reorder_func_choice = "None",
  show_error_bars = TRUE,
  ylab = 'Fraction Mean', 
  xlab = 'Fraction Type by Group',
  title = 'Tissue type fractions by group'
)

gives error message

Error in embed_notebook(iatlas.modules::plotly_bar(plot_data = barplot_df, :
could not find function "embed_notebook"

embed_notebook called within definition of notebook_barplot in iatlas-notebooks/functions/notebook_functions.R

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