Related
As far as I can find, there is only one tutorial about loading Seurat objects into WGCNA (https://ucdavis-bioinformatics-training.github.io/2019-single-cell-RNA-sequencing-Workshop-UCD_UCSF/scrnaseq_analysis/scRNA_Workshop-PART6.html). I am really new to programming so it's probably just my inexperience, but I am not sure how to load my Seurat object into a format that works with WGCNA's tutorials (https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/).
Here is what I have tried thus far:
This tries to replicate datExpr and datTraits from part I.1:
library(WGCNA)
library(Seurat)
#example Seurat object -----------------------------------------------
ERlist <- list(c("CPB1", "RP11-53O19.1", "TFF1", "MB", "ANKRD30B",
"LINC00173", "DSCAM-AS1", "IGHG1", "SERPINA5", "ESR1",
"ILRP2", "IGLC3", "CA12", "RP11-64B16.2", "SLC7A2",
"AFF3", "IGFBP4", "GSTM3", "ANKRD30A", "GSTT1", "GSTM1",
"AC026806.2", "C19ORF33", "STC2", "HSPB8", "RPL29P11",
"FBP1", "AGR3", "TCEAL1", "CYP4B1", "SYT1", "COX6C",
"MT1E", "SYTL2", "THSD4", "IFI6", "K1AA1467", "SLC39A6",
"ABCD3", "SERPINA3", "DEGS2", "ERLIN2", "HEBP1", "BCL2",
"TCEAL3", "PPT1", "SLC7A8", "RP11-96D1.10", "H4C8",
"PI15", "PLPP5", "PLAAT4", "GALNT6", "IL6ST", "MYC",
"BST2", "RP11-658F2.8", "MRPS30", "MAPT", "AMFR", "TCEAL4",
"MED13L", "ISG15", "NDUFC2", "TIMP3", "RP13-39P12.3", "PARD68"))
tnbclist <- list(c("FABP7", "TSPAN8", "CYP4Z1", "HOXA10", "CLDN1",
"TMSB15A", "C10ORF10", "TRPV6", "HOXA9", "ATP13A4",
"GLYATL2", "RP11-48O20.4", "DYRK3", "MUCL1", "ID4", "FGFR2",
"SHOX2", "Z83851.1", "CD82", "COL6A1", "KRT23", "GCHFR",
"PRICKLE1", "GCNT2", "KHDRBS3", "SIPA1L2", "LMO4", "TFAP2B",
"SLC43A3", "FURIN", "ELF5", "C1ORF116", "ADD3", "EFNA3",
"EFCAB4A", "LTF", "LRRC31", "ARL4C", "GPNMB", "VIM",
"SDR16C5", "RHOV", "PXDC1", "MALL", "YAP1", "A2ML1",
"RP1-257A7.5", "RP11-353N4.6", "ZBTB18", "CTD-2314B22.3", "GALNT3",
"BCL11A", "CXADR", "SSFA2", "ADM", "GUCY1A3", "GSTP1",
"ADCK3", "SLC25A37", "SFRP1", "PRNP", "DEGS1", "RP11-110G21.2",
"AL589743.1", "ATF3", "SIVA1", "TACSTD2", "HEBP2"))
genes = c(unlist(c(ERlist,tnbclist)))
mat = matrix(rnbinom(500*length(genes),mu=500,size=1),ncol=500)
rownames(mat) = genes
colnames(mat) = paste0("cell",1:500)
sobj = CreateSeuratObject(mat)
sobj = NormalizeData(sobj)
sobj$ClusterName = factor(sample(0:1,ncol(sobj),replace=TRUE))
sobj$Patient = paste0("Patient", 1:500)
sobj = AddModuleScore(object = sobj, features = tnbclist,
name = "TNBC_List",ctrl=5)
sobj = AddModuleScore(object = sobj, features = ERlist,
name = "ER_List",ctrl=5)
#WGCNA -----------------------------------------------------------------
sobjwgcna <- sobj
sobjwgcna <- FindVariableFeatures(sobjwgcna, selection.method = "vst", nfeatures = 2000,
verbose = FALSE, assay = "RNA")
options(stringsAsFactors = F)
sobjwgcnamat <- GetAssayData(sobjwgcna)
datExpr <- t(sobjwgcnamat)[,VariableFeatures(sobjwgcna)]
datTraits <- sobjwgcna#meta.data
datTraits = subset(datTraits, select = -c(nCount_RNA, nFeature_RNA))
I then copy-paste the code as written in the WGCNA I.2a tutorial (https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/FemaleLiver-02-networkConstr-auto.pdf), and that all works until I get to this line in the I.3 tutorial (https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/FemaleLiver-03-relateModsToExt.pdf):
MEList = moduleEigengenes(datExpr, colors = moduleColors)
Error in t.default(expr[, restrict1]) : argument is not a matrix
I tried converting both moduleColors and datExpr into a matrix with as.matrix(), but the error still persists.
Hopefully this makes sense, and thanks for reading!
So doing as.matrix(datExpr) right after datExpr <- t(sobjwgcnamat)[,VariableFeatures(sobjwgcna)] worked. I had been trying it right before MEList = moduleEigengenes(datExpr, colors = moduleColors)
and that didn't work. Seems simple but order matters I guess.
all!
I came here because I have one problem bugging me for quite some time now. I am using love2d engine as a 'graphical' addition to lua scripting, but this problem is of lua type (I believe, at least).
I have a function:
createNew_keepOld = function (oldImgData, oldImgDraw)
local newImgData = oldImgData --I am assigning old value to another variable
local newImgDraw = oldImgDraw --I am doing the same thing as with data
for x = 0, newImgData:getWidth()-1 do
for y = 0, newImgData:getHeight()-1 do
local r, g, b, a = newImgData:getPixel(x, y)
r = 2*r
g = 2*g
b = 0.5*b
a = 2*a
newImgData:setPixel(x, y, r, g, b, a)
end
end
newImgDraw:replacePixels(newImgData)
return newImgData, newImgDraw
end
When this code finishes, I get the change I need, but not WHERE I want it. I just want to produce two new variables which will store data and image objects. But, in process, original image gets changed.
Is there any way to declare:
name = function (const param, const param)
return some_things
end
So that I get output I need without changing the original stuff? Or is there some problem with my code that I cannot see?
Thanks!
Actually the nature of this problem is both in Love2D and Lua. Anyway.
Quote from Lua Reference Manual 5.3:
Tables, functions, threads, and (full) userdata values are objects: variables do not actually contain these values, only references to them. Assignment, parameter passing, and function returns always manipulate references to such values; these operations do not imply any kind of copy.
Most types from Love2D are of userdata Lua type, so when passing them to your function you are actually passing reference to them, hence you modify the "old" versions in the very end. Those types usually have functions made for copying them.
ImageData does have one and Image does not, but you can do the following:
createNew_keepOld = function (oldImgData, oldImgDraw)
local newImgData = oldImgData:clone()
for x = 0, newImgData:getWidth()-1 do
for y = 0, newImgData:getHeight()-1 do
local r, g, b, a = newImgData:getPixel(x, y)
r = 2*r
g = 2*g
b = 0.5*b
a = 2*a
newImgData:setPixel(x, y, r, g, b, a)
end
end
local newImgDraw = love.graphics.newImage(newImgData, oldImgDraw:getFlags())
return newImgData, newImgDraw
end
Note that I created entirely new Image based on copied ImageData and image flags from the old one.
In Lua when you make a variable equal to a table value you are not copying or duplicating that information. The new variable simply points to the same values as the other variable.
Example:
tbl1 = {}
tbl2 = tbl1
tbl2[1] = 1
print(tbl1[1])
In order to create a newImgDatabased on oldImgData you need to preform a deep copy:
function deepcopy(orig)
local orig_type = type(orig)
local copy
if orig_type == 'table' then
copy = {}
for orig_key, orig_value in next, orig, nil do
copy[deepcopy(orig_key)] = deepcopy(orig_value)
end
setmetatable(copy, deepcopy(getmetatable(orig)))
else -- number, string, boolean, etc
copy = orig
end
return copy
end
Resource for table copying: Lua-Users Wiki: Copy Table
This Solution only works a table type, it will not work for userdata
How can I get variables that not declared yet?
Here are simple example:
a = b
b = 123
What I want from these 2 lines is a << 123. But obv it doesn't work.
I know the easy way to get the answer a = 123 is cut 1st line and paste it to lower than 2nd line.
But I'm in some problem. I need some function like 'WillDeclaredVar()' that I can use in like this:
a = WillDeclaredVar(b)
sheepCount = 123
b = sheepCount
print(a)
so I can get the answer '123'.
Or there are any built-in functions that will allows me to do similar thing?
===
I think the link given by timrau is not telling my case. the key point is how to get Variables 'that not declared yet'.
===
Adding actual Code:
triggerCount = 0 -- Counting number of 'Trigger' function
local Trigger = function (t)
triggerCount = triggerCount + 1
return Trigger (t)
end
-- following Triggers are same as while statement.
-- following Triggers doing: Add 1 MarineCount until get 64000 MarineCount
Trigger { -- Here the Trigger function. Now triggerCount = 1.
players = {P1}
actions = {
SetDeaths(P1, Add, 1, "Terran Marine")
},
flag = {preserved},
}
Portal(LoopStart);
-- function Portal(VariableName) returns VariableName = triggerCount. So LoopStart = 1.
Trigger { -- Now triggerCount = 2.
players = {P1}
actions = {
LinkList(LoopEnd, LoopStart);
-- function LinkList(From, To) changes 'From' Trigger's next pointer to the 'To' Trigger.
-- But now the problem happens. Because 'LoopEnd' is not declared yet.
},
flag = {preserved},
}
Trigger { -- Now triggerCount = 3.
players = {P1}
conditions = {
Deaths(P1, Exactly, 64000, "Terran Marine");
}
actions = {
_LinkList(LoopEnd);
-- Reset LoopEnd's next pointer(= LoopEscape) if MarineCount hits 64000
},
flag = {preserved},
}
Portal(LoopEnd); -- LoopEnd = 3.
Changing Order of Triggers will break the Trigger logic(while statement).
All i want is get easy to coding. To put in bluntly, I don't need to solve this problem(get undeclared var). I can imagine a few ways to avoid it. But if i using these ways then the coding work will be very complicated and the difficulty of coding will increases greatly. The difficulty made me stop coding in recent months.
How can I get variables that not declared yet?
Short of time travel, you can't.
Your example code doesn't explain the motivation for the question, because this:
a = WillDeclaredVar(b)
sheepCount = 123
b = sheepCount
print(a)
Can trivially be rearranged into this:
sheepCount = 123
b = sheepCount
a = WillDeclaredVar(b)
print(a)
It would be easier to answer your question if you showed the actual problem you're trying to solve (to avoid an XY problem).
However, as stated there are few things we can note.
First, you need to distinguish between declaring a variable and giving it a value. In Lua you can say:
local b
To declare b as a local variable, which presumably will make a slot for it in the stack frame and let you bind closures to it, before you give it a value. However, the line:
a = WillDeclaredVar(b)
Will pass WillDeclaredVar the value that b currently has, and there's no way for a to change retroactively as a result of b being assigned a new value. That's simply not going to happen, ever. Neither a nor WillDeclaredVar are even aware that b exists, they are receive the value it contains at the point of call.
You could however bind the variable b to a closure which will fetch b's current value when needed.
-- declare b before giving it a value, aka "forward reference"
local b
a = function() return b end
sheepCount = 123
b = sheepCount
print(a()) -- call a to get b's current value
Another way to do that would be to make b a global variable, which is really just a key into your environment table, so you could say:
a = WillDeclaredVar('b')
And have a be some object that can fetch the current value of __ENV['b'] when required.
However, neither of these will support this syntax:
print(a)
a needs to be a function, something that looks up the value of b when needed rather than simply holding a previously computed value. You could do it in this particular instance (i.e. a needs to be convertable to a string), by creating a proxy object that implements __tostring.
function WillDeclaredVar(variableName)
local proxy = { environment = _ENV or _G, variableName = variableName }
return setmetatable(proxy, {
__tostring = function(proxy)
return proxy.environment[proxy.variableName]
end
})
end
-- a will compute a value based on the current value of b when needed
a = WillDeclaredVar('b')
sheepCount = 123
b = sheepCount
print(a)
Output:
123
To make var1 be a reference for var2 write var1 = ReferenceF or var2 (please note a space inside "ReferenceFor"!)
do
local values, references, reference_flag = {}, {}
setmetatable(_G, {
__index = function (_, name)
if name == 'ReferenceF' then
reference_flag = true
elseif reference_flag then
reference_flag = false
return {[references] = name}
elseif references[name] then
return _G[references[name]]
else
return values[name]
end
end,
__newindex = function (_, name, val)
if type(val) == 'table' and val[references] then
references[name] = val[references]
else
values[name] = val
end
end
})
end
a = ReferenceF or b -- a is Reference For b
b = ReferenceF or c -- b is Reference For c
sheepCount = 123
c = sheepCount
print(a, b, c) --> 123 123 123
I am playing with records and list. Please, I want to know how to use one variable twice. When I assign any values into variable _list and after that I try rewrite this variable then raising error:
** exception error: no match of right hand side value
-module(hello).
-author("anx00040").
-record(car, {evc, type, color}).
-record(person, {name, phone, addresa, rc}).
-record(driver, {rc, evc}).
-record(list, {cars = [], persons = [], drivers = []} ).
%% API
-export([helloIF/1, helloCase/1, helloResult/1, helloList/0, map/2, filter/2, helloListCaA/0, createCar/3, createPerson/4, createDriver/2, helloRecords/0, empty_list/0, any_data/0, del_Person/1, get_persons/1, do_it_hard/0, add_person/2]).
createCar(P_evc, P_type, P_color) -> _car = #car{evc = P_evc, type = P_type, color = P_color}, _car
.
createPerson(P_name, P_phone, P_addres, P_rc) -> _person= #person{name = P_name, phone = P_phone, addresa = P_addres, rc = P_rc}, _person
.
createDriver(P_evc, P_rc) -> _driver = #driver{rc = P_rc, evc = P_evc}, _driver
.
empty_list() ->
#list{}.
any_data() ->
_car1 = hello:createCar("BL 4", "Skoda octavia", "White"),
_person1 = hello:createPerson("Eduard B.","+421 917 111 711","Kr, 81107 Bratislava1", "8811235"),
_driver1 = hello:createDriver(_car1#car.evc, _person1#person.rc),
_car2 = hello:createCar("BL 111 HK", "BMW M1", "Red"),
_person2 = hello:createPerson("Lenka M","+421 917 111 111","Krizn0, 81107 Bratislava1", "8811167695"),
_driver2 = hello:createDriver(_car2#car.evc, _person2#person.rc),
_car3 = hello:createCar("BL 123 AB", "Audi A1 S", "Black"),
_person3 = hello:createPerson("Stela Ba.","+421 918 111 711","Azna 20, 81107 Bratislava1", "8811167695"),
_driver3 = hello:createDriver(_car3#car.evc, _person3#person.rc),
_list = #list{
cars = [_car1,_car2,_car3],
persons = [_person1, _person2, _person3],
drivers = [_driver1, _driver2, _driver3]},
_list.
add_person(List, Person) ->
List#list{persons = lists:append([Person], List#list.persons) }.
get_persons(#list{persons = P}) -> P.
do_it_hard()->
empty_list(),
_list = add_person(any_data(), #person{name = "Test",phone = "+421Test", addresa = "Testova 20 81101 Testovo", rc =88113545}),
io:fwrite("\n"),
get_persons(add_person(_list, #person{name = "Test2",phone = "+421Test2", addresa = "Testova 20 81101 Testovo2", rc =991135455}))
.
But it raising error when i use variable _list twice:
do_it_hard()->
empty_list(),
_list = add_person(any_data(), #person{name = "Test",phone = "+421Test", addresa = "Testova 20 81101 Testovo", rc =88113545}),
_list =add_person(_list, #person{name = "Test2",phone = "+421Test2", addresa = "Testova 20 81101 Testovo2", rc =991135455}),
get_persons(_list)
.
In the REPL, it can be convenient to experiment with things while re-using variable names. There, you can do f(A). to have Erlang "forget" the current assignment of A.
1> Result = connect("goooogle.com").
{error, "server not found"}
2> % oops! I misspelled the server name
2> f(Result).
ok
3> Result = connect("google.com").
{ok, <<"contents of the page">>}
Note that this is only a REPL convenience feature. You can't do this in actual code.
In actual code, variables can only be assigned once. In a procedural language (C, Java, Python, etc), the typical use-case for reassignment is loops:
for (int i = 0; i < max; i++) {
conn = connect(servers[i]);
reply = send_data(conn);
print(reply);
}
In the above, the variables i, conn, and reply are reassigned in each iteration of the loop.
Functional languages use recursion to perform their loops:
send_all(Max, Servers) ->
send_loop(1, Max, Servers).
send_loop(Current, Max, _Servers) when Current =:= Max->
ok;
send_loop(Current, Max, Servers) ->
Conn = connect(lists:nth(Current, Servers)),
Reply = send_data(Conn),
print(Reply).
This isn't very idiomatic Erlang; I'm trying to make it mirror the procedural code above.
As you can see, I'm getting the same effect, but my assignments within a function are fixed.
As a side note, you are using a lot of variable names beginning with underscore. In Erlang this is a way of hinting that you will not be using the value of these variables. (Like in the above example, when I've reached the end of my list, I don't care about the list of servers.) Using a leading underscore as in your code turns off some useful compiler warnings and will confuse any other developers who look at your code.
In some situations it is convenient to use use SeqBind:
SeqBind is a parse transformation that auto-numbers all occurrences of these bindings following the suffix # (creating L#0, L#1, Req#0, Req#1) and so on.
Simple example:
...
-compile({parse_transform,seqbind}).
...
List# = lists:seq(0, 100),
List# = lists:filter(fun (X) -> X rem 2 == 0 end, List#)
...
I used google...
Erlang is a single-assignment language. That is, once a variable has been given a value, it cannot be given a different value. In this sense it is like algebra rather than like most conventional programming languages.
http://www.cis.upenn.edu/~matuszek/General/ConciseGuides/concise-erlang.html
I try to use rCharts package to create interactive graphs. I used tutorials examples but I have not managed to use nPlot method. It did not return error but I did not receive the figure as they did in the tutorial.
require(devtools)
install_github('rCharts', 'ramnathv')
library(rCharts)
a<-as.data.frame(HairEyeColor)
hair_eye_male<-subset(a, Sex=="Male")
is.data.frame(hair_eye_male)
n1<-nPlot(Freq~Hair, group='Eye', data=hair_eye_male, type="multiBarChart")
n1
hair_eye = as.data.frame(HairEyeColor)
p2 <- nPlot(Freq ~ Hair, group = 'Eye',
data = subset(hair_eye, Sex == "Female"),
type = 'multiBarChart'
)
p2$chart(color = c('brown', 'blue', '#594c26', 'green'))
p2
in the Environment panel n1 and p2 appeared as Environment. I tried rChart and it works.
Best regards