... | ... |
@@ -55,7 +55,7 @@ install_github("RGLab/openCyto", ref="trunk") |
55 | 55 |
### Installing from [BioConductor](https://www.bioconductor.org). |
56 | 56 |
|
57 | 57 |
- [Current BioConductor |
58 |
- Relase](https://doi.org/doi:10.18129/B9.bioc.CytoML) |
|
58 |
+ Release](https://doi.org/doi:10.18129/B9.bioc.CytoML) |
|
59 | 59 |
|
60 | 60 |
<!-- end list --> |
61 | 61 |
|
... | ... |
@@ -83,7 +83,7 @@ BiocManager::install("CytoML", version = "devel") |
83 | 83 |
<!-- end list --> |
84 | 84 |
|
85 | 85 |
``` r |
86 |
-install.packges("devtools") |
|
86 |
+install.packages("devtools") |
|
87 | 87 |
devtools::install_github("RGLab/CytoML", ref = "trunk") |
88 | 88 |
``` |
89 | 89 |
|
... | ... |
@@ -92,7 +92,7 @@ devtools::install_github("RGLab/CytoML", ref = "trunk") |
92 | 92 |
<!-- end list --> |
93 | 93 |
|
94 | 94 |
``` r |
95 |
-install.packges("devtools") |
|
95 |
+install.packages("devtools") |
|
96 | 96 |
devtools::install_github("RGLab/CytoML@*release") |
97 | 97 |
``` |
98 | 98 |
|
... | ... |
@@ -209,7 +209,7 @@ plotGate(gh) |
209 | 209 |
|
210 | 210 |
Because CytoML and flowWorkspace reproduce the entire analysis in a |
211 | 211 |
workspace in R, we have access to information about which cells are part |
212 |
-of which cell popualtions. |
|
212 |
+of which cell populations. |
|
213 | 213 |
|
214 | 214 |
flowWorkspace has convenience methods to extract the cells from specific |
215 | 215 |
cell populations: |
... | ... |
@@ -324,7 +324,7 @@ GatingSet2flowJo(gs, outFile) |
324 | 324 |
## Next Steps |
325 | 325 |
|
326 | 326 |
See the [flowWorskspace](http://www.github.com/RGLab/flowWorkspace) and |
327 |
-\[openCyto\](<http://www.github.com/RGLab/openCyto>\] packages to learn |
|
327 |
+[openCyto](http://www.github.com/RGLab/openCyto] packages to learn |
|
328 | 328 |
more about what can be done with `GatingSet` objects. |
329 | 329 |
|
330 | 330 |
## Code of conduct |
... | ... |
@@ -439,9 +439,16 @@ public: |
439 | 439 |
caltbl.setY(y); |
440 | 440 |
caltbl.setX(x); |
441 | 441 |
unsigned nX = x.size(); |
442 |
- bt->maxValue = caltbl.getX()[nX-1]; |
|
443 |
- bt->channelRange = caltbl.getY()[nX-1]; |
|
442 |
+ if(nX==0) |
|
443 |
+ {//assign the default values when caltbl is not present in xml |
|
444 |
+ bt->maxValue = 262144; |
|
445 |
+ bt->channelRange = 4096; |
|
444 | 446 |
|
447 |
+ }else |
|
448 |
+ { |
|
449 |
+ bt->maxValue = caltbl.getX()[nX-1]; |
|
450 |
+ bt->channelRange = caltbl.getY()[nX-1]; |
|
451 |
+ } |
|
445 | 452 |
transformation * curTran = bt; |
446 | 453 |
/* |
447 | 454 |
* sometime, the biexp parameters may not be stored properly |