I am consitently getting the following error message, which I cannot understand:
Checking if input is properly formatted...
Detected "Custom" file_type flag, looking for correct column names...
Did not detect silent mutations in input, is this expected?Calculating frequency of mutations...
The melt generic in data.table has been passed a table and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace like reshape2::melt(mutation_counts). In the next version, this warning will become an error.setting mutation hierarchy...
The dcast generic in data.table has been passed a data.frame and will attempt to redirect to the reshape2::dcast; please note that reshape2 is deprecated, and this redirection is now deprecated as well. Please do this redirection yourself like reshape2::dcast(x). In the next version, this warning will become an error.Defining a palette in mainPalette is recommended when file_type is set to "Custom", defaulting to a predefined palette with 20 levelsNULL
I am following the following tutorial to create a waterfall plot: https://genviz.org/module-03-genvisr/0003/02/01/waterfall_GenVisR/
My code is listed below:
library(GenVisR) library(reshape2) library(gridExtra) set.seed(426) myVars <- slx_merged %>% select("Sample", "Gene symbol", "Consequence", "Protein effect") myVars <- rename(myVars, c("sample"="Sample")) myVars <- rename(myVars, c("gene"=Gene symbol)) myVars <- rename(myVars, c("variant_class"="Consequence")) myVars <- rename(myVars, c("amino.acid.change"=Protein effect`))mutation_priority <- as.character(unique(myVars$variant_class)) myVars <- myVars %>% filter(amino.acid.change!= "NA") waterfall(myVars, fileType = "Custom", variant_class_order=mutation_priority)I am consitently getting the following error message, which I cannot understand:
Checking if input is properly formatted... Detected "Custom" file_type flag, looking for correct column names... Did not detect silent mutations in input, is this expected?Calculating frequency of mutations... The melt generic in data.table has been passed a table and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached, e.g. melt.list, you can prepend the namespace like reshape2::melt(mutation_counts). In the next version, this warning will become an error.setting mutation hierarchy... The dcast generic in data.table has been passed a data.frame and will attempt to redirect to the reshape2::dcast; please note that reshape2 is deprecated, and this redirection is now deprecated as well. Please do this redirection yourself like reshape2::dcast(x). In the next version, this warning will become an error.Defining a palette in mainPalette is recommended when file_type is set to "Custom", defaulting to a predefined palette with 20 levels NULL
I'd be grateful for an explanation please.
Thank you.