Pathview: empty metabolic map
0
0
Entering edit mode
landenshanie ▴ 40
@landenshanie-23570
Last seen 16 months ago
Australia

I am trying to use pathview to do this (example from https://pathview.r-forge.r-project.org/):

enter image description here

However, I am getting empty circles (all white) and my pathview output file has "NA" for all mol.data and "#FFFFFF" for mol.col

I assume that I am just inputting my data fundamentally incorrectly but I have tried searching the vignette, posts, and doing everything I can think of and I cant figure out why my circles wont get colored in.

This is my code:

temp<-pathview(gene.data = df_pathview[,2],gene.idtype="KEGG", pathway.id = "01100", species = "hsa")

This is how my gene.data df looks:

head(df_pathview)

gene average.mean.diff

3706 ITPKA -1.4976111

2686 GGT7 -8.0186713

216 ALDH1A1 -10.0488333

As you can see my rownames are the entrezIDs and column 2 is my effect sizes (numerics ranging from - to +). Are my entrez ID's not the write IDs to input? I got them with this code:

genekegglinks=getGeneKEGGLinks(species.KEGG = "hsa",convert=FALSE)

Any help would be greatly appreciated as I'm dying to get this metabolic map to work!

Here is my session info:

sessionInfo() R version 4.0.2 (2020-06-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.5 LTS

Matrix products: default BLAS: /usr/lib/x8664-linux-gnu/blas/libblas.so.3.7.1 LAPACK: /usr/lib/x8664-linux-gnu/lapack/liblapack.so.3.7.1

locale: [1] LCCTYPE=enAU.UTF-8 LCNUMERIC=C
[3] LC
TIME=enAU.UTF-8 LCCOLLATE=enAU.UTF-8
[5] LC
MONETARY=enAU.UTF-8 LCMESSAGES=enAU.UTF-8
[7] LC
PAPER=enAU.UTF-8 LCNAME=C
[9] LCADDRESS=C LCTELEPHONE=C
[11] LCMEASUREMENT=enAU.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] annotate1.66.0 XML3.99-0.5 org.Hs.eg.db3.11.4 [4] AnnotationDbi1.50.3 IRanges2.22.2 S4Vectors0.26.1
[7] Biobase2.48.0 BiocGenerics0.34.0 limma3.44.3
[10] pathview
1.28.1 readxl1.3.1 dplyr1.0.2
[13] biomaRt_2.45.5

loaded via a namespace (and not attached): [1] KEGGgraph1.48.0 Rcpp1.0.5 prettyunits1.1.1
[4] png
0.1-7 Biostrings2.56.0 assertthat0.2.1
[7] digest0.6.25 BiocFileCache1.12.1 R62.4.1
[10] cellranger
1.1.0 RSQLite2.2.1 httr1.4.2
[13] ggplot23.3.2 pillar1.4.6 zlibbioc1.34.0
[16] rlang
0.4.8 progress1.2.2 curl4.3
[19] rstudioapi0.11 Rgraphviz2.32.0 blob1.2.1
[22] stringr
1.4.0 munsell0.5.0 RCurl1.98-1.2
[25] bit4.0.4 compiler4.0.2 pkgconfig2.0.3
[28] askpass
1.1 openssl1.4.3 tidyselect1.1.0
[31] KEGGREST1.28.0 gridExtra2.3 tibble3.0.3
[34] viridisLite
0.3.0 fansi0.4.1 crayon1.3.4
[37] dbplyr1.4.4 bitops1.0-6 rappdirs0.3.1
[40] grid
4.0.2 gtable0.3.0 xtable1.8-4
[43] lifecycle0.2.0 DBI1.1.0 magrittr1.5
[46] scales
1.1.1 graph1.66.0 cli2.0.2
[49] stringi1.5.3 XVector0.28.0 viridis0.5.1
[52] xml2
1.3.2 ellipsis0.3.1 generics0.0.2
[55] vctrs0.3.4 tools4.0.2 bit644.0.5
[58] glue
1.4.2 purrr0.3.4 hms0.5.3
[61] colorspace1.4-1 memoise1.1.0

pathview • 1.1k views
ADD COMMENT

Login before adding your answer.

Traffic: 758 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6