AlexanderPico commented 6 years ago

As discussed with Marco, this PR replaces with pathway example with real pathways from WikiPathways.

Attached are replacement images for this section of the vignette using the same png filenames to simplify replacement. onco-pathway-1 onco-pathway-viz-1 onco-pathway-viz2-1

AlexanderPico commented 6 years ago

Travis is failing. One reason is that rWikiPathways isn't installed. I only added library(rWikiPathways). If you want to have a more complete installation in the vignette, simply add:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("rWikiPathways")

codecov-io commented 6 years ago

Codecov Report

Merging #112 into master will decrease coverage by 0.18%. The diff coverage is n/a.

@@            Coverage Diff             @@
##           master     #112      +/-   ##
==========================================
- Coverage   70.52%   70.33%   -0.19%     
==========================================
  Files          21       21              
  Lines        7768     7768              
==========================================
- Hits         5478     5464      -14     
- Misses       2290     2304      +14

Impacted Files	Coverage Δ
R/prim.algorithm.R	`79.11% <0%> (-7.6%)`	:arrow_down:
R/bootstrap.R	`86.58% <0%> (-0.64%)`	:arrow_down:

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danro9685 commented 5 years ago

Replaced by #113

BIMIB-DISCo / TRONCO

added real pathways from wikipathways to vignette #112

Codecov Report