... | ... |
@@ -78,8 +78,10 @@ exportMethods(runParams) |
78 | 78 |
exportMethods(sampleLabel) |
79 | 79 |
import(Rcpp) |
80 | 80 |
import(RcppEigen) |
81 |
+import(data.table, except = melt) |
|
81 | 82 |
import(foreach) |
82 | 83 |
import(ggplot2) |
84 |
+import(grDevices) |
|
83 | 85 |
import(graphics) |
84 | 86 |
import(grid) |
85 | 87 |
import(gridExtra, except = c(combine)) |
... | ... |
@@ -117,6 +119,7 @@ importFrom(methods,is) |
117 | 119 |
importFrom(methods,new) |
118 | 120 |
importFrom(plyr,mapvalues) |
119 | 121 |
importFrom(reshape2,melt) |
122 |
+importFrom(scales,brewer_pal) |
|
120 | 123 |
importFrom(scales,dscale) |
121 | 124 |
importFrom(scales,hue_pal) |
122 | 125 |
importFrom(stringi,stri_list2matrix) |
... | ... |
@@ -26,7 +26,7 @@ |
26 | 26 |
#' clusterDiffexpRes = differentialExpression(celdaCGSim$counts, |
27 | 27 |
#' celdaCGMod, c1 = c(1, 2)) |
28 | 28 |
#' @export |
29 |
-#' @importFrom data.table as.data.table |
|
29 |
+#' @rawNamespace import(data.table, except = melt) |
|
30 | 30 |
#' @importFrom MAST FromMatrix |
31 | 31 |
#' @importFrom MAST zlm |
32 | 32 |
#' @importFrom MAST summary |
... | ... |
@@ -81,7 +81,7 @@ differentialExpression <- function(counts, |
81 | 81 |
# explicitly load library SummarizedExperiment due to MAST package |
82 | 82 |
# dependency error |
83 | 83 |
library(SummarizedExperiment) |
84 |
- |
|
84 |
+ |
|
85 | 85 |
sca <- suppressMessages(MAST::FromMatrix(log_normalized_mat, cdat)) |
86 | 86 |
cdr2 <- colSums(SummarizedExperiment::assay(sca) > 0) |
87 | 87 |
SummarizedExperiment::colData(sca)$cngeneson <- scale(cdr2) |
... | ... |
@@ -216,6 +216,7 @@ plotDimReduceFeature <- function(dim1, |
216 | 216 |
#' This matrix should be the same as the one used to generate `celdaMod`. |
217 | 217 |
#' @param celdaMod Celda object of class "celda_G" or "celda_CG". |
218 | 218 |
#' @param modules Character vector. Module(s) from celda model to be plotted. |
219 |
+#' e.g. c("1", "2"). |
|
219 | 220 |
#' @param rescale Logical. |
220 | 221 |
#' Whether rows of the matrix should be rescaled to [0, 1]. Default TRUE. |
221 | 222 |
#' @param size Numeric. Sets size of point on plot. Default 1. |
... | ... |
@@ -237,7 +238,7 @@ plotDimReduceFeature <- function(dim1, |
237 | 238 |
#' plotDimReduceModule( |
238 | 239 |
#' dim1 = celdaTsne[, 1], dim2 = celdaTsne[, 2], |
239 | 240 |
#' counts = celdaCGSim$counts, celdaMod = celdaCGMod, |
240 |
-#' modules = c("L1", "L2")) |
|
241 |
+#' modules = c("1", "2")) |
|
241 | 242 |
#' @export |
242 | 243 |
plotDimReduceModule <- |
243 | 244 |
function(dim1, |
... | ... |
@@ -252,6 +253,7 @@ plotDimReduceModule <- |
252 | 253 |
colorLow = "grey", |
253 | 254 |
colorMid = NULL, |
254 | 255 |
colorHigh = "blue") { |
256 |
+ |
|
255 | 257 |
factorized <- factorizeMatrix(celdaMod = celdaMod, |
256 | 258 |
counts = counts) |
257 | 259 |
matrix <- factorized$proportions$cell |
... | ... |
@@ -585,6 +585,7 @@ vplayout <- function(x, y) { |
585 | 585 |
#' @importFrom gtable gtable_height |
586 | 586 |
#' @importFrom gtable gtable_width |
587 | 587 |
#' @importFrom gtable gtable_add_grob |
588 |
+#' @import grDevices |
|
588 | 589 |
.heatmapMotor <- function(matrix, |
589 | 590 |
borderColor, |
590 | 591 |
cellWidth, |
... | ... |
@@ -1218,6 +1219,7 @@ vplayout <- function(x, y) { |
1218 | 1219 |
} |
1219 | 1220 |
|
1220 | 1221 |
#' @importFrom scales dscale |
1222 |
+#' @importFrom scales brewer_pal |
|
1221 | 1223 |
.generateAnnotationColours <- function(annotation, |
1222 | 1224 |
annotationColors, |
1223 | 1225 |
drop) { |
... | ... |
@@ -1265,7 +1267,7 @@ vplayout <- function(x, y) { |
1265 | 1267 |
factorColors <- factorColors[-ind] |
1266 | 1268 |
} else { |
1267 | 1269 |
annotationColors[[names(annotation)[i]]] <- |
1268 |
- brewer_pal("seq", contCounter)(5)[seq(4)] |
|
1270 |
+ scales::brewer_pal("seq", contCounter)(5)[seq(4)] |
|
1269 | 1271 |
contCounter <- contCounter + 1 |
1270 | 1272 |
} |
1271 | 1273 |
} |
... | ... |
@@ -23,7 +23,8 @@ This matrix should be the same as the one used to generate `celdaMod`.} |
23 | 23 |
|
24 | 24 |
\item{celdaMod}{Celda object of class "celda_G" or "celda_CG".} |
25 | 25 |
|
26 |
-\item{modules}{Character vector. Module(s) from celda model to be plotted.} |
|
26 |
+\item{modules}{Character vector. Module(s) from celda model to be plotted. |
|
27 |
+e.g. c("1", "2").} |
|
27 | 28 |
|
28 | 29 |
\item{rescale}{Logical. |
29 | 30 |
Whether rows of the matrix should be rescaled to [0, 1]. Default TRUE.} |
... | ... |
@@ -61,5 +62,5 @@ celdaTsne <- celdaTsne(counts = celdaCGSim$counts, |
61 | 62 |
plotDimReduceModule( |
62 | 63 |
dim1 = celdaTsne[, 1], dim2 = celdaTsne[, 2], |
63 | 64 |
counts = celdaCGSim$counts, celdaMod = celdaCGMod, |
64 |
- modules = c("L1", "L2")) |
|
65 |
+ modules = c("1", "2")) |
|
65 | 66 |
} |