My University is testing blackboard ultra. I generate the exercises with
exams2blackboard("ProbEjemploPrueba9", n=10, fix_pre = TRUE, converter = "pandoc", encoding = "utf8", eval = list(partial = T, negative = T, rule = "false"))
but when I use the $ in $A$, it does not leave space, it appears like this;
"IfA is the event .... "instead of "If A is the event.... "
I attach the image.
The solution is to remove $, because in this case nothing happens, but maybe other times it is necessary.
Would there be any solution to fix that typo?
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.
I want to display a decomposition wavelet in 3 level.
so can any help me in give a Matlab function to display it?
[cA cH cV cD]=dwt2(a,waveletname);
out=[cA cH;cV cD];
figure;imshow(out,[]);
That only works for the first level.
actually, I want to representation square mode such wavemenu in Matlab.
example of the view decomposition
I am fairly new to it.
thanx.
You should use the function wavedec2(Image,numberOfLevels,'wname') with the amount of levels that you need.
For more information look at
http://www.mathworks.com/help/wavelet/ref/wavedec2.html
Code for example with db1
clear all
im = imread('cameraman.tif');
[c,s] = wavedec2(im,3,'db1');
A1 = appcoef2(c,s,'db1',1);
[H1,V1,D1] = detcoef2('all',c,s,1);
A2 = appcoef2(c,s,'db1',2);
[H2,V2,D2] = detcoef2('all',c,s,2);
A3 = appcoef2(c,s,'db1',3);
[H3,V3,D3] = detcoef2('all',c,s,3);
V1img = wcodemat(V1,255,'mat',1);
H1img = wcodemat(H1,255,'mat',1);
D1img = wcodemat(D1,255,'mat',1);
A1img = wcodemat(A1,255,'mat',1);
V2img = wcodemat(V2,255,'mat',1);
H2img = wcodemat(H2,255,'mat',1);
D2img = wcodemat(D2,255,'mat',1);
A2img = wcodemat(A2,255,'mat',1);
V3img = wcodemat(V3,255,'mat',1);
H3img = wcodemat(H3,255,'mat',1);
D3img = wcodemat(D3,255,'mat',1);
A3img = wcodemat(A3,255,'mat',1);
mat3 = [A3img,V3img;H3img,D3img];
mat2 = [mat3,V2img;H2img,D2img];
mat1 = [mat2,V1img;H1img,D1img];
imshow(uint8(mat1))
The final result
While finding follow sets, rules such as
A->aA can lead to infinite recursion. Is there any coding technique to avoid it?
Note that the above example is just an example, in practice such a recursion could happen indirectly as well.
Here is my sample C code for finding follow sets. The grammar is stored as an array of linked lists. Please tell me if the code is unclear at any point.
set findFollowSet(char nonTerminal[], Grammar G, hashTable2 h) //later assume that all first sets are already in the hashtable.
{
LINK temp1 = find2(h, nonTerminal);
set s= createEmptySet();
set temp = createEmptySet();
char lhs[80] = "\0";
int i;
//special case
if(temp1->numRightSideOf==0) //its not on right side of any grammar rule
return insert(s, "$");
for(i=0;i<temp1->numRightSideOf;i++)
{
link l = G.rules[temp1->rightSideOf[i]];
strcpy(lhs, l->symbol); //storing the lhs just in case the nonTerm appears on the rightmost end of the rule.
printf("!!!!! %s\n", lhs);
sleep(1);
//finding nonTerminal in G
while(l!=NULL)
{
if(strcmp(l->symbol, nonTerminal) == 0)
break;
l=l->next;
}
//found the nonTerminal in G
if(l->next!=NULL)
{
temp = findFirstSet(l->next, G, h);
temp = removeElement(temp, "EPSILON");
}
else //its on the rightmost end of the rule
temp = findFollowSet(lhs, G, h);
s = setUnion(s, temp); destroySet(temp);
}
return s;
}
FIRST and FOLLOW sets are defined recursively, so you need to find the recursive closure. What this mean in practice is that you don't find the FOLLOW set for a single non-terminal -- you find all the FOLLOW sets for all the terminals simultaneously, by starting with all sets empty and going over the grammar adding symbols to different sets, until no more symbols can be added to any set. So you end up with something like:
FOLLOW[*] = {}; // all follow sets start empty
done = false;
while (!done)
done = true;
for (R : each rule in the grammar)
A = RHS[R];
tmp = FOLLOW[A];
for (S : each symbol in LHS[R] from right to left)
if (S is terminal)
tmp = {S};
else
if (!(FOLLOW[S] contains tmp))
done = false
FOLLOW[S] |= tmp
if (epsilon in FIRST[S])
tmp |= FIRST[S] - epsilon
else
tmp = FIRST[S]
Ok I got the answer but its inefficient.
So if anyone wants to suggest some more efficient answer, please feel welcomed.
Just store the recursion stack explicitly and at each recursive call, check if the entry already exists in the stack.
Mind you, you need to check the entire stack not just the top of it.