Question

STRINGdb v.2.16.4 does not render the plot [libpng error: Not a PNG file]

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h.valipour.k • 0

@hvalipourk-16085

Last seen 6 months ago

Australia

Hi everyone,

Since I have installed the newest STRINGdb package, the following command does not render the plot.

string_db$plot_network(hits, add_link = TRUE, add_summary = TRUE)

It complains like below:

libpng error: Not a PNG file

The installation was on Bioconductor 3.18.

Any thoughts?

STRINGdb • 507 views

ADD COMMENT • link updated 6 months ago by damian.szk ▴ 110 • written 6 months ago by h.valipour.k • 0

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Write what version of the package you are using? (the newest one is on Bioconductor 3.19).

Make sure the "hits" object is not empty and if not and also make sure you do not initiate the stringdb object module with an "http" parameter.

If this is all correct, please write more information, so I can debug the issue (is it a vignette you are trying to run, and if not does it run as is?)

ADD REPLY • link 6 months ago damian.szk ▴ 110

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Thank you for your assistance.

I wanted to confirm that the issue was resolved by removing the protocol = "http" parameter when initialising STRINGdb. Here's the change that worked:

From:

string_db <- STRINGdb$new(version = "12", species = SP_ID, score_threshold = 400, input_directory = "", protocol = "http")

To:

string_db <- STRINGdb$new(version = "12", species = SP_ID, score_threshold = 400, input_directory = "")

This adjustment allowed the plot to display correctly, even in Bioconductor version 3.18, after installing STRINGdb version 2.16.4 from a local source with:

install.packages("STRINGdb_2.16.4.tar.gz", repos = NULL, type = "source")

I appreciate your guidance on this matter!

ADD REPLY • link 6 months ago h.valipour.k • 0

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Great. Thanks for the update!

ADD REPLY • link 6 months ago damian.szk ▴ 110