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gregtbooth / Pombe_PROseq

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Seeking Guidance on Generating Heatmaps #1

Open Will19902225 opened 10 months ago

Will19902225 commented 10 months ago

I'm interested in generating a heatmap similar to those seen in figure fig.3b or figure fig.2c from your publication with PMID: 29416031, utilizing code for cut-seq or ChIP-seq signal visualization. However, I've been unable to locate the specific code here used to generate these heatmaps. Could you recommend a method or specific tools that could help create such heatmaps for this purpose?

gregtbooth commented 10 months ago

Hi, The code for those plots should be in the code in this repository named "FCheatMaps_v3.R". It should have what you need to make the heatmaps.

Will19902225 commented 10 months ago

Hi,

Thank you for your response. I've encountered an issue while running the code "source("Target folder/GB_Functions.R")". Specifically, an error related to the 'bigWig' library has surfaced, indicating that there's no package available with the name "bigWig." Despite attempting to install the 'bigWig' package, I've been unsuccessful in locating it.

Additionally, I've been trying to execute the FCheatMaps_v3.R code as a positive control before utilizing our own data. However, I've encountered difficulty in locating the 'bw' file when running "bwpath = "/Users/gregorybooth/Google\ Drive/SEAGATE_EXP/Fisher_collaboration/alignment/bw/". There are around 100 bw files needed. Like: 5993_7157_26977_HJ72CBGXX_pombe_WT_COMBINED_DMSO_CAGATC_R1.fastq_pombe_plus.bw and ePROseq_Pombe_CDK9as_0min_DMSO_COMBINED_pombe_plus.bw, et. al. I noticed there are some 'bw' files on GitHub, but their names differ from the ones I mentioned.

Could you please provide me with the relevant file(s) so that I can smoothly execute your code and replicate the program?