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How to define colors for clinical features that use continuous values

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### Discussed in https://github.com/PoisonAlien/maftools/discussions/1051 Originally posted by **juferban** September 21, 2024 Hi, I tried to add clinicalFeatures to my oncoplot that are continuous variables. While I manage to do it,...

PoisonAlien

**Describe the issue** There is an issue with gtMarkers and the underlying C code of how the function is executed. This results in an error of ```` *** caught segfault...

grantn5

**So I loaded my GISTIC2.0 results via the following command:** laml_gistic = readGistic(gisticAllLesionsFile = "C:/Users/.../all_lesions.conf_90.txt", gisticAmpGenesFile = "C:/Users/.../amp_genes.conf_90.txt", gisticDelGenesFile = "C:/Users/.../del_genes.conf_90.txt", gisticScoresFile = "C:/Users/.../scores.gistic") **and created my ChromPlot using:** gisticChromPlot(laml_gistic,...

HummelFa

Provenance of PFAM Domains is Unclear

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I see `system.file('extdata', 'protein_domains.RDs', package = 'maftools')` but how old is it? `?pfamDomains` does not explain version.

DarioS

Colors applied to continuous clinicalFeatures in Oncoplot are not right

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Hello, I am having an issue when I try to add colors for continuous clinical features to my Oncoplot. When I order the samples in a way other than based...

Willem50

annovarToMaf with table = "ensGene" wrong

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Dear author, Hello and thank you for developing the tool. I am currently encountering an issue with annovarToMaf. When I run Annovar to annotate with refGene and use `table =...

HuZhuocheng

mafCompare may yield biased results when comparing cohorts with unequal sample sizes due to absolute mutation count-based Fisher test

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The current maftools::mafCompare() function performs Fisher's exact test using raw mutation counts (e.g., MutatedSamples) without accounting for cohort sample size disparities. This could lead to misleading statistical significance when: Cohort...

fengqlin

The SNV statistics does not match with bcftools stats

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I see that maftools is inaccurately estimating the number of `T>C` and `C>T` and other statistics in SNV Class plot. I am also attaching the VCF file and MAF file...

Rohit-Satyam

**Describe the issue** Running prepareMutSig requires R.Utils to read a file. This is not included in the conda installed version. `conda create --name maftools -c conda-forge -c bioconda r-base r-maftools`...

dansteiert

Missing sampels in clinical data causing wrong prevalence calculated

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**Describe the issue** Some sampels is missing from the clinical data if no mutations were found. This will make prevalence looks higher than the actual number. **Command** ``` maf =...

sainadfensi