deprecate Taxa names -> Features

[himmil]

No description provided.

[himmil]

@TuomasBorman can you merge?

[TuomasBorman]

Tests (tests/testthat directory) seems still have deprecated functions

[TuomasBorman]

Related to what we discussed today; to replace aes_string:

There are two cases where we have used aes_string: "the standard way", i.e. case 1, and with do.call function, i.e., case 3

Below you will find, how to replace these

library(ggplot2)

data(cars)


######################### CASE 1
p <- ggplot(cars)

p + geom_point(aes(x = speed, y = dist))

p + geom_point(aes_string(x = "speed", y = "dist"))

p + geom_point(aes(x = .data[["speed"]], y = .data[["dist"]]))

######################### CASE2

p + aes(x = speed, y = dist) + geom_point()

p + aes_string(x = "speed", y = "dist") + geom_point()

p + aes(x = .data[["speed"]], y = .data[["dist"]]) + geom_point()

############################ CASE 2.1

aesthetic <- aes(x = speed, y = dist)
p + aesthetic + geom_point()

aesthetic <- aes_string(x = "speed", y = "dist")
p + aesthetic + geom_point()


aesthetic <- aes(x = .data[["speed"]], y = .data[["dist"]])
p + aesthetic + geom_point()

################# CASE 3

# IS not working
args <- list(x = "speed", y = "dist")
aesthetic <- do.call(aes, args)
p + aesthetic + geom_point()

# Works
args <- list(x = "speed", y = "dist")
aesthetic <- do.call(aes_string, args)
p + aesthetic + geom_point()

# Option 1 (I think this is better)
args <- list(x = "speed", y = "dist")
args <- lapply(args, function(x) if (!is.null(x)) sym(x))
aesthetic <- do.call(aes, args)
p + aesthetic + geom_point()

# Option 2
args <- list(x = "speed", y = "dist")
args <- lapply(args, function(x) if (!is.null(x)) sym(x))
aesthetic <- aes(!!!args)
p + aesthetic + geom_point()

[TuomasBorman]

Error occurs when the data is loaded

no visible global function --> add importFrom tags (check other functions for example)

[himmil]

Now, finally, it should be ready to be merged.

[TuomasBorman]

Sorry for late reply. Can you run BiocCheck::BiocCheck(). It seems that the indentation is off (should be multiplication of 4 spaces)

[TuomasBorman]

After indentation check, this is good to go

[himmil]

Hi, I ran the check and it gave an error that installation calls found in vignettes. How should I fix it?

[TuomasBorman]

You can skip those errors not directly related to this PR. We can fix those things in other PRs

[himmil]

Ok, this is ready to be merged (I don't have write access to do it).