From c0b4574801909e6aa260374d920a2f00bc84acaf Mon Sep 17 00:00:00 2001 From: Georgios Voloudakis Date: Tue, 14 Jan 2025 14:48:27 -0500 Subject: [PATCH] Readme improvements --- README.md | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index b8aa964..6d705e1 100644 --- a/README.md +++ b/README.md @@ -212,8 +212,9 @@ A few useful column definitions across files are the following: Average rank (`AvgRank`) distribution plots are also generated for diagnostic purposes. Please note that when using cluster comparison signatures, the z-scores of the disease signatures and the `AvgRank` distributions may not be normally distributed, but the pipeline is non-parametric and can accomodate for that. -![CDR AvgRank Distribution](/data-raw/RA_cdr_AvgRank_distribution_landscape.png) -![GTP AvgRank Distribution](/data-raw/RA_gtp_AvgRank_distribution_landscape.png) +![CDR AvgRank Distribution](/data-raw/readme.images/RA_cdr_AvgRank_distribution_landscape.png) + +![GTP AvgRank Distribution](/data-raw/readme.images/RA_gtp_AvgRank_distribution_landscape.png) # STEP 4: Additional figures Additional figures can be prepared @@ -231,7 +232,8 @@ showcase_method_cdr_gtp( ) ``` -![actinomycin D in RA](/data-raw/RA.STARNET_BLD.actinomycin-d.CRCGN004_PC3_6H.BRD-A42383464-001-04-8.10.png) + +![actinomycin D in RA](/data-raw/readme.images/RA.STARNET_BLD.actinomycin-d.CRCGN004_PC3_6H.BRD-A42383464-001-04-8.10.png) ## Generating a gene-target prioritization plot ``` @@ -244,6 +246,7 @@ gtp_pvalue_qqplot( ### Parameters figure.name = "gtp_actions", # main body of the name of the figure ) ``` -In this there is no actionable gene that demonstrates a FDR-significant compbined score while also having FDR-significant dysregulation in the disease signatures and antagonism via shRNA/overexpression/CRISPR -![actinomycin D in RA](/data-raw/prioritization.stouffer.scaled.before.png) +In this there is no actionable gene that demonstrates a FDR-significant compbined score while also having FDR-significant dysregulation in the disease signatures and antagonism via shRNA/overexpression/CRISPR. + +![actinomycin D in RA](/data-raw/readme.images/prioritization.stouffer.scaled.before.png)